[OnePlus 3 & 3T Cross Device Development] :
So removing some stuff from /system/app or /system/priv-app is no problem as I understand your last edit because /system itself is clean, right?

Issue could be my build.prop additions, but those are not important for me, I can leave them out if necessary.

Here the script I am using. Not the nicest, but working for me.

Not using gapps, microG and other stuff, unfortunately have to use Magisk at the moment because LOS does have issues with some banking apps.

In the past I updated my install every day/week or whatever was the update rate of the OS. At this moment I am trying to minimize it to once a month after AOSP security update is out, also to prevent degradation of disk (especially in combination with cleaning caches, removing app caches etc... but I like a clean setup...).

#!/sbin/sh
#
# Script by 2Tweak
# Last modified 18-05-2019

clear 2>/dev/null
mount /system 2>/dev/null

# app list to remove
applist="
/system/app/AntHalService
/system/app/BasicDreams
/system/app/BuiltInPrintService
/system/app/Calendar
/system/app/CtsShimPrebuilt
/system/app/EasterEgg
/system/app/Email
/system/app/ExactCalculator
/system/app/Exchange2
/system/app/HTMLViewer
/system/app/Jelly
/system/app/LatinIME
/system/app/LiveWallpapersPicker
/system/app/LockClock
/system/app/messaging
/system/app/PhotoTable
/system/app/PrintRecommendationService
/system/app/Stk
/system/app/Terminal
/system/app/Traceur
/system/app/WallpaperBackup
/system/priv-app/AudioFX
/system/priv-app/BackupRestoreConfirmation
/system/priv-app/CallLogBackup
/system/priv-app/CNEService
/system/priv-app/CtsShimPrivPrebuilt
/system/priv-app/Contacts
/system/priv-app/DocumentsUI
/system/priv-app/Eleven
/system/priv-app/InputDevices
/system/priv-app/ManagedProvisioning
/system/priv-app/OneplusDoze
/system/priv-app/OneplusPocketMode
/system/priv-app/OneTimeInitializer
/system/priv-app/Gallery2
/system/priv-app/SharedStorageBackup
/system/priv-app/Tag
/system/priv-app/Updater
/system/priv-app/UserDictionaryProvider
/system/priv-app/VpnDialogs
/system/priv-app/WeatherProvider
/system/priv=app/WfdService
/system/media/bootanimation.zip
/system/bin/bootanimation
"

# /system/app/NfcNci >> resulting in crash on profiles setting
# /system/priv-app/SettingsIntelligence >> resulting in slow settings menu
# /system/priv-app/WallpaperCropper >> resulting in reboot at fresh install

# file list to cleanup
filelist="
/cache/*
/data/anr/*
/data/backup/*
/data/cache/*
/data/dalvik-cache/*
/data/lost+found/*
/data/tombstones/*
/data/backup/pending/*
/data/local/tmp/*
/data/system/dropbox/*
/data/system/procstats/*
/data/system/usagestats/daily/*
/data/system/usagestats/0/monthly/*
/data/system/usagestats/0/weekly/*
/data/system/usagestats/0/yearly/*
/data/system/last-fstrim
/data/system/install_sessions.xml
/data/system/uiderrors.txt
"

echo
echo "############################################"
echo "# ROM DEBLOAT SCRIPT #"
echo "############################################"
echo

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

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

for appname in $applist
do
chmod -rf 777 $appname 2>/dev/null
rm -rf $appname 2>/dev/null
done
echo " done!"

echo -n "Removing junk files..................."
for filename in $filelist
do
chmod -rf 777 $filename 2>/dev/null
rm -rf $filename 2>/dev/null
done

echo " done!"

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

echo -n "Clearing all app caches..............."

for i in $(ls /data/data/ 2>/dev/null)
do
chmod -rf 777 /data/data/$i/cache 2>/dev/null
rm -rf /data/data/$i/cache/* 2>/dev/null
rm -rf /data/data/$i/code_cache/* 2>/dev/null
done

echo " done!"

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

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

chmod 400 /data/system/dropbox 2>/dev/null
chmod 400 /data/system/procstats 2>/dev/null
chmod 400 /data/system/usagestats/0/daily 2>/dev/null
chmod 400 /data/system/usagestats/0/monthly 2>/dev/null
chmod 400 /data/system/usagestats/0/weekly 2>/dev/null
chmod 400 /data/system/usagestats/0/yearly 2>/dev/null

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, checks and sending data
logcat.live=disable
persist.android.strictmode=0
profiler.force_disable_err_rpt=1
profiler.force_disable_ulog=1
ro.config.nocheckin=1
ro.kernel.android.checkjni=0
ro.kernel.checkjni=0

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

# Improve call quality
ro.ril.enable.amr.wideband=1

# Optimize Dalvik
dalvik.vm.dexopt-flags=v=n,o=v,m=y

# Some tweaks to save battery
pm.sleep_mode=1
power.saving.mode=1
ro.ril.disable.power.collapse=0
ro.config.hw_power_saving=1
ro.mot.eri.losalert.delay=1000
wifi.supplicant_scan_interval=300

# End of my settings
' >> $fname 2>/dev/null
chmod 644 $fname 2>/dev/null

echo " done!"

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

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

rm -f /system/vendor/etc/gps.conf 2>/dev/null
touch /system/vendor/etc/gps.conf 2>/dev/null
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 2>/dev/null
chmod 644 /system/vendor/etc/gps.conf 2>/dev/null

echo " done!"

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

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

rm -f /data/local/userinit.sh 2>/dev/null
touch /data/local/userinit.sh 2>/dev/null
echo '#!/system/bin/sh
# My settings

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

# Enable power_efficient workqueue
echo 1 > /sys/module/workqueue/parameters/power_efficient

# Battery tweaks
echo 500 > /proc/sys/vm/dirty_expire_centisecs
echo 1000 > /proc/sys/vm/dirty_writeback_centisecs

# End of my settings
' > /data/local/userinit.sh 2>/dev/null
chmod 777 /data/local/userinit.sh 2>/dev/null

echo " done!"

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

echo -n "Trimming SSD storage.................."

fstrim -v /data 2>/dev/null
fstrim -v /cache 2>/dev/null
fstrim -v /system 2>/dev/null

echo " done!"

echo