The point is, this should not happen to core functionality. Specially not sneaky like this.

Define core functionality. We are carrying computers that happen to have a radio that can communicate with cell towers. The phone functionality is just as "core" as any other service that the OS exposes. (Camera, Web Browser, GPS)

It's still called a "phone", and it really sucks at being a computer (it is a good entertainment device though). Since a lot of things are still done over phone calls and every citizen in a civilized country is expected to be in possession of a phone number, I'd qualify it as core functionality.

If it's in the /system partition, it shouldn't be able to do any data collection or bound to any companies' services.

Anything bound to any companies' services or doing any data collection should be entirely user-controlled and user-replacable.