Assuming the joint is otherwise intact, I can't see big turbo being responsible for boot failure unless it forced some (possibly small) piece of the joint to fracture and fly off, puncturing that boot. In this case I can understand why they would say that warranty is contingent upon disassembly and inspection of the joint though, it's possible that the boot may have been inadvertently punctured in the course of performing the work on the car; in which case no warranty on that part and labor to replace it regardless. Now if they refuse to warranty your Sync system because you installed BT, then that's another matter.