Before my current
MCS i had a 53 plate two years ago. This was modified with some GTT parts (IC, oil catch can, induction fit etc) and also had AP Brakes and Leda Coilovers.
I had it services a few times at Stephen James BMW in Keston (now closed) and they never had any issues. They also seemed more interested in the car. I'd watch the miles when you put it in for a service - mine had 10 miles more on it once and they said it needed road testing for the tracking - long road test!!
I also had a few things done under warranty, but as they were unrelated to the moddified parts it wasn't an issue, i.e. tailgate lifters and rear wiper motor.