[Xiaomi Redmi Note 3 Guides, News, & Discussion] roasm:
This is the result of many work hours and reflashes after brick, enjoy!

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1) on the phone

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Security > Permissions > Allow root (must be china dev rom and unlocked bootloader to be availabile)

Display > Color & Contrast > Standard (Disable automatic contrast)

Lock screen & Fingerprint > Sleep > Set display 2 minutes delay

Sync > Off

Privacy > AD personalisation > Turn Off

Battery & performance > Battery indicator > percentage

Battery & performance > Manage battery usage > Off

Battery & performance > Hide system animations

Developer options > Enable USB debugging

Developer options > Disable MIUI optimizations

Transfer on the phone and install the following apk:

Install MiXplorer Beta 6

Install "WSZF root uninstaller"

Activate app MiXplorer & WSZF as ROOT

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2) from computer, with phone connected

make /system partition modifiable

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adb root

adb disable-verity

adb reboot

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3) delete from /system/app with app "MiXplorer"

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AMAPNetworkLocation

AnalyticsCore

AntHalService

Antispam

AntiTheftDemo

BarcodeScanner

BasicDreams

BatteryGuruSystemApp

BugReport

CloudService

DataMonitor

Email

FileExplorer

Galaxy4

GameCenter

GuardProvider

HoloSpiralWallpaper

jjcontainer

jjhome

jjknowledge

jjstore

KingSoftCleaner

LiveWallpapers

LiveWallpapersPicker

Metok

MiLinkService

Mipay

MiuiCompass

MiuiVideo

MiWallpaper

NetworkAssistant2

NoiseField

Notes

PaymentService

PhaseBeam

PhotoTable

PowerKeeper

QtiBackupAgent

QtiFeedback

QuickSearchBox

SecurityAdd

SystemAdSolution

ThemeManager

TrafficControl

VisualizationWallpapers

VoiceAssist

Whetstone

XiaomiAccount

XiaomiVip

XMPass

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4) delete from /system/priv-app with app "MiXplorer"

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Backup

BackupRestoreConfirmation

BatterySaver

Browser

CellBroadcastReceiver

CleanMaster

CloudBackup

FindDevice

MiDrop

MiGameCenterSDKService

Mipub

MiuiVoip

Music

WallpaperCropper

Weather

WeatherProvider

YellowPage

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5) delete from /system/data-app with "MiXplorer"

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delete everything from here, is full of spyware!

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6) delete from /cust/app/customized with app "MiXplorer"

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delete everything from here, is full of spyware!

also erase this too:

/etc/WhetstonePermission delete

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7) disable autoruns with Autorun Manager Pro v4.3.96_upload_by_NF.apk

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App Store, disable all intents

Updater, disable all intents

Xiaomi service framework, disable all intent's and make it frozen

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8) install from f-droid an open source firewall to disable everything except browser, email, dns, etc (apps installed by you, not the default ones

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Only in the above conditions I can say that the phone is secure.

Everything works after that: GPS, Dual SIM, Internet, fingerprint unlock, etc.