TL,DR: New phone Xiaomi Redmi 5 (german provider) Magisk and TWRP installed, ROM completely stock MIUI Global (Android Nougat 7.1.2) does not receive every SMS / 50% loss

My girlfriend has changed her phone. The phone Number previously was registered for Signal. She unregistered her number from Signal so the SMS can be received from provider.

The problem is, sending and receiving SMS works fine - everytime we are testing. But late in evening (only when she not used her phone) and over night, it seems the SMS are blocked in some way.

I still get transmission report immediately for each SMS (which is not the case when phone switched off) but she never receive the messages. I can call her and after talking the SMS sending/receiving works again, except for the lost messages.

The SMS messages also appear in stock SMS app (she uses Textra now), except for the lost messages.

She already disabled the blocking list in MIUI Security Center (never used at all).

SecurityCenter.apk can not be disabled/frozen from adb shell. After uninstalling the phone does not boot anymore.

Can MIUI 10 run without this app? How can the SecurityCenter.apk be disabled/uninstalled safely?

Why does phone not boot anymore? Is Magisk disabling DM-Verity by default for the whole System, or maybe just for Magisk itself only (checkbox is unchecked)?

Is this SMS blocking issue maybe related to power management / deep sleep?

Must she allow all permissions to the SecurityCenter.apk to make SMS work?

To clarify, the phone is not messed up with Magisk, no system apps deleted, no Xposed modules installed. in fact Magisk is not really used, just RootExplorer has granted permissions, but never used

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