[OnePlus 3 & 3T Cross Device Themes, Apps & Mods] :
After some reading and some input from people like @anupritaisno1 I came to the next setup.

I went back to rootless, encrypted my phone and made two scripts instead of one.

The install.sh script is used after installing the firmware, rom and kernel (normal dirty flashes) and is only removing the packages I am not using as some log files, and other useless stuff. Also used to implement some tweaks (userinit.sh, gps.conf, build.prop).

The cleanup.sh script is a script for removing all cache, dalvik-cache, app-caches etc.. and is the part I was only using about once a month to start almost clean without loosing settings.

install.sh, used to remove packages I am not using, some logging and other stuff, implementing some tweaks (userinit.sh):

#!/sbin/sh
#
# Script by 2Tweak
# Last modified 07-09-2019

################################################

# First setup
clear

echo
echo "##########################################"
echo "# DEBLOAT AND TWEAK SCRIPT #"
echo "##########################################"
echo

mount -o remount,rw /cache
mount -o remount,rw /data
mount -o remount,rw /sdcard
mount -o remount,rw /system

################################################

echo -n "Shrinking ROM to the bare minimum..."

# app list to remove
applist="
AntHalService
AudioFX
BasicDreams
BluetoothMidiService
BookmarkProvider
BuiltInPrintService
Calendar
CaptivePortalLogin
CNEService
CallLogBackup
CellBroadcastReceiver
CompanionDeviceManager
Contacts
CtsShimPrebuilt
CtsShimPrivPrebuilt
DocumentsUI
EasterEgg
Eleven
Email
ExactCalculator
Exchange2
Gallery2
HTMLViewer
InputDevices
Jelly
LineageSetupWizard
LiveWallpapersPicker
LockClock
ManagedProvisioning
OneTimeInitializer
PhotoTable
PrintRecommendationService
SharedStorageBackup
SimAppDialog
Stk
Tag
Terminal
Traceur
Updater
UserDictionaryProvider
VpnDialogs
WallpaperBackup
WfdService
"

for appname in $applist
do
if [ -e /system/app/$appname ]; then
chmod -R 777 /system/app/$appname
rm -rf /system/app/$appname
fi
if [ -e /system/priv-app/$appname ]; then
chmod -R 777 /system/priv-app/$appname
rm -rf /system/priv-app/$appname
fi
done

echo " done!"

################################################

echo -n "Removing unneeded and junk files...."

# file list to cleanup
filelist="
/cache
/data/anr
/data/backup
/data/lineageos_updates
/data/local/tmp
/data/lost+found
/data/misc/bootstat
/data/ota
/data/ota_package
/data/system/batterystats.bin
/data/system/dropbox
/data/system/graphicsstats
/data/system/install_sessions.xml
/data/system/last-fstrim
/data/system/procstats
/data/system/syncmanager-log
/data/system/uiderrors.txt
/data/system/usagestats/0/daily
/data/system/usagestats/0/monthly
/data/system/usagestats/0/weekly
/data/system/usagestats/0/yearly
/data/tombstones
/system/bin/bootanimation
/system/media/bootanimation.zip
"

for filename in $filelist
do
if [ -d $filename ]; then
chmod -R 777 $filename
rm -rf $filename/*
fi
if [ -f $filename ]; then
chmod 777 $filename
rm -f $filename
fi
done

# Remove bak, log, tmp files
find /data -iname "*.bak" -type f -exec rm -f {} +
find /data -iname "*.log" -type f -exec rm -f {} +
find /data -iname "*.tmp" -type f -exec rm -f {} +

find /system -iname "*.bak" -type f -exec rm -f {} +
find /system -iname "*.log" -type f -exec rm -f {} +
find /system -iname "*.tmp" -type f -exec rm -f {} +

echo " done!"

################################################

echo -n "Cleaning app data..................."

for i in $(ls /data/data/)
do
if [ -e /data/data/$i/app_webview ]; then
chmod -R 777 /data/data/$i/app_webview
# keep cookies for webapp logins
if [ -e /data/data/$i/app_webview/Cookies ]; then
mv -f /data/data/$i/app_webview/Cookies /data/local/tmp/$i.Cookies
fi
rm -rf /data/data/$i/app_webview/*
if [ -e /data/local/tmp/$i.Cookies ]; then
mv -f /data/local/tmp/$i.Cookies /data/data/$i/app_webview/Cookies
fi
fi
done

for k in $(ls /sdcard/Android/data/)
do
if [ -e /sdcard/Android/data/$k/cache ]; then
chmod -R 777 /sdcard/Android/data/$k/cache
rm -rf /sdcard/Android/data/$k/cache/*
fi
done

echo " done!"

################################################

echo -n "Optimizing app databases............"

# Optimize databases
for i in $(find /data -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

for i in $(find /sdcard -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

echo " done!"

################################################

echo -n "Setting log permissions read-only..."

chmod 000 /data/tombstones
chmod 000 /data/system/dropbox
chmod 000 /data/system/graphicsstats
chmod 000 /data/system/procstats
chmod 000 /data/system/usagestats/0/daily
chmod 000 /data/system/usagestats/0/weekly
chmod 000 /data/system/usagestats/0/monthly
chmod 000 /data/system/usagestats/0/yearly

echo " done!"

################################################

echo -n "Adding my build.prop settings......."

fname="/system/build.prop"
tmpvar=$(sed '/.*My settings.*/{s///;q;}' $fname | sed '$d')
echo "$tmpvar" > $fname
echo '
# My settings

# Disable multi user
fw.max_users=1
fw.show_multiuserui=0
fw.show_hidden_users=0
fw.power_user_switcher=0

# Disable logging
logcat.live=disable

# Disable boot animation
debug.sf.nobootanimation=1

# Disable USB debugging notification
persist.adb.notify=0

# Enable VoLTE
persist.dbg.ims_volte_enable=1
persist.dbg.volte_avail_ovr=1
persist.dbg.vt_avail_ovr=1
persist.dbg.wfc_avail_ovr=1
persist.radio.rat_on=combine
persist.radio.data_ltd_sys_ind=1
persist.radio.data_con_rprt=1
persist.radio.calls.on.ims=1

# End of my settings
' >> $fname
chmod 644 $fname

echo " done!"

################################################

echo -n "Adding my gps.conf settings........."

rm -f /system/vendor/etc/gps.conf
touch /system/vendor/etc/gps.conf
echo '# My settings

# NTP Server - only one allowed!
NTP_SERVER=nl.pool.ntp.org

# Debug level
DEBUG_LEVEL=0

# End of my settings
' > /system/vendor/etc/gps.conf
chmod 644 /system/vendor/etc/gps.conf

echo " done!"

################################################

echo -n "Adding my userinit.sh settings......"

echo '#!/system/bin/sh
# My settings

# Optimize databases
for i in $(find /data -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

for i in $(find /storage/emulated/0 -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

# Disable iostats
chmod 666 /sys/block/sda/queue/iostats
echo "0" > /sys/block/sda/queue/iostats
chmod 444 /sys/block/sda/queue/iostats

# Disable some wakelocks
if [ -e /sys/devices/virtual/misc/boeffla_wakelock_blocker ]; then
echo "IPA_WS;NETLINK;bms;netmgr_wl;qcom_rx_wakelock;sensor_SMD;wlan;wlan_extscan_wl;wlan_ipa;wlan_pno_wl;wlan_wow_wl" > /sys/devices/virtual/misc/boeffla_wakelock_blocker/wakelock_blocker
fi

# End of my settings
' > /data/local/userinit.sh
chmod 777 /data/local/userinit.sh

echo " done!"

echo

cleanup.sh, used about once a month to have the feeling I start with an almost clean system (probably useless):

]#!/sbin/sh
#
# Script by 2Tweak
# Last modified 06-09-2019

################################################

# First setup
clear

echo
echo "##########################################"
echo "# DEEP CLEAN SCRIPT #"
echo "##########################################"
echo

mount -o remount,rw /cache
mount -o remount,rw /data
mount -o remount,rw /sdcard
mount -o remount,rw /system

################################################

echo -n "Removing unneeded and junk files...."

# file list to cleanup
filelist="
/cache
/data/anr
/data/backup
/data/cache
/data/dalvik-cache
/data/lineageos_updates
/data/local/tmp
/data/lost+found
/data/misc/bootstat
/data/ota
/data/ota_package
/data/resource-cache
/data/system/batterystats.bin
/data/system/dropbox
/data/system/graphicsstats
/data/system/install_sessions.xml
/data/system/last-fstrim
/data/system/package_cache
/data/system/procstats
/data/system/syncmanager-log
/data/system/uiderrors.txt
/data/system/usagestats/0/daily
/data/system/usagestats/0/monthly
/data/system/usagestats/0/weekly
/data/system/usagestats/0/yearly
/data/tombstones
/system/bin/bootanimation
/system/media/bootanimation.zip
"

for filename in $filelist
do
if [ -d $filename ]; then
chmod -R 777 $filename
rm -rf $filename/*
fi
if [ -f $filename ]; then
chmod 777 $filename
rm -f $filename
fi
done

# Remove bak, log, tmp and dex files
find /data -iname "*.bak" -type f -exec rm -f {} +
find /data -iname "*.log" -type f -exec rm -f {} +
find /data -iname "*.tmp" -type f -exec rm -f {} +
find /data -iname "*.odex" -type f -exec rm -f {} +
find /data -iname "*.vdex" -type f -exec rm -f {} +

find /system -iname "*.bak" -type f -exec rm -f {} +
find /system -iname "*.log" -type f -exec rm -f {} +
find /system -iname "*.tmp" -type f -exec rm -f {} +

# Some other useless system related files
rm -f /data/stock_boot_*.img.gz
rm -rf /system/vendor/overlay

echo " done!"

################################################

echo -n "Cleaning app data and caches........"

for i in $(ls /data/data/)
do
if [ -e /data/data/$i/cache ]; then
chmod -R 777 /data/data/$i/cache
rm -rf /data/data/$i/cache/*
fi
if [ -e /data/data/$i/code_cache ]; then
chmod -R 777 /data/data/$i/code_cache
rm -rf /data/data/$i/code_cache/*
fi
if [ -e /data/data/$i/files/.Fabric ]; then
chmod -R 777 /data/data/$i/files/.Fabric
rm -rf /data/data/$i/files/.Fabric/*
fi
if [ -e /data/data/$i/files/cache ]; then
chmod -R 777 /data/data/$i/files/cache
rm -rf /data/data/$i/files/cache/*
fi
if [ -e /data/data/$i/app_webview ]; then
chmod -R 777 /data/data/$i/app_webview
# keep cookies for webapp logins
if [ -e /data/data/$i/app_webview/Cookies ]; then
mv -f /data/data/$i/app_webview/Cookies /data/local/tmp/$i.Cookies
fi
rm -rf /data/data/$i/app_webview/*
if [ -e /data/local/tmp/$i.Cookies ]; then
mv -f /data/local/tmp/$i.Cookies /data/data/$i/app_webview/Cookies
fi
fi
done

for k in $(ls /sdcard/Android/data/)
do
if [ -e /sdcard/Android/data/$k/cache ]; then
chmod -R 777 /sdcard/Android/data/$k/cache
rm -rf /sdcard/Android/data/$k/cache/*
fi
done

echo " done!"

################################################

echo -n "Cleaning app oat files.............."

for j in $(ls /data/app/)
do
if [ -e /data/app/$j/oat/arm ]; then
chmod -R 777 /data/app/$j/oat/arm
rm -rf /data/app/$j/oat/arm/*
fi
if [ -e /data/app/$j/oat/arm64 ]; then
chmod -R 777 /data/app/$j/oat/arm64
rm -rf /data/app/$j/oat/arm64/*
fi
done

echo " done!"

################################################

echo -n "Remove some app specific files......"

# App specific
rm -rf /data/data/org.fdroid.fdroid/files/*.apk
rm -rf /data/data/org.videolan.vlc/app_vlc/*

echo " done!"

################################################

echo -n "Remove empty directories............"

# Remove empty directories
find /data/data -type d -depth -exec rmdir {} + 2>/dev/null
find /sdcard -type d -depth -exec rmdir {} + 2>/dev/null

echo " done!"

################################################

echo -n "Optimizing app databases............"

# Optimize databases
for i in $(find /data -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

for i in $(find /sdcard -iname "*.db" -type f)
do
sqlite3 $i "VACUUM;" 2>/dev/null
sqlite3 $i "REINDEX;" 2>/dev/null
done

echo " done!"

################################################

echo -n "Setting log permissions read-only..."

chmod 000 /data/tombstones
chmod 000 /data/system/dropbox
chmod 000 /data/system/graphicsstats
chmod 000 /data/system/procstats
chmod 000 /data/system/usagestats/0/daily
chmod 000 /data/system/usagestats/0/weekly
chmod 000 /data/system/usagestats/0/monthly
chmod 000 /data/system/usagestats/0/yearly

echo " done!"

echo

My setup now:

Oxygen 9.05 firmware

op3_recovery 3.3.1-0 from @anupritaisno1

Lineage OS 16

Flash kernel 3.18.140

No Google stuff, using FDroid and Aurora Store as playstores.

The idea was to have a topic where also other people would share their scripts, tweaks etc...

Am I really the only one tweaking a little around??