Following this logic, when your gearbox fails, they can say it's because of your phone connected to USB for Android Auto, or power supply for dashcam.
MIB3 can detect if speakers are not connected at all, but not if they have different impedance. So no, system will not show or log any errors. But if you are unsure, i can try to check with OBD11 for any errors related to speakers, maybe tomorrow.
Tracking down ECU to different speakers sounds like a magic to me, as speakers have NOTHING to do with CAN bus, which is only common point of ECU and MIB.
Forget about Canton speakers. They will not bring any improvement, as they are mediocre at best. "Magic" of canton is additional power amp with DSP and Dolby Prologic.
If you are worried about warranty, leave it alone till car is under warranty.
But i don't think you should be...