I think it's a CYA thing. Most service departments aren't up on aftermarket gear and what the OEM components are rated for. All they know is "if it's not BMW it's bad."
I went through a warranty issue with BMW for one of my old installers and you can elevate this to a regional guy who can reinstate certain parts of the warranty. It kept my installer from having to pay 10 large to have his car rewired to have his warranty reinstated on his entire electrical system. The OEM navi failed in his 3-series and when he took it in they said it was because we had installed aftermarket amps and speakers, like they're even remotely interrelated. it took some arguing and prrof from our side but it can be done.
I'd gather up as much evidence as you can supporting your case and schedule an appt. with the regional warranty guy. Good luck.