The OP stated he had purchased the extended maintenance plan. Rotors will be replaced only when they wear beyond acceptable limits - otherwise, BMW will not reimburse the dealer. And "hassling" your dealer seems like a great way to quickly get on their s--t list, which you really don't want to do while under warranty & covered maintenance.
But it does no harm to request a brake inspection due to the noise. At the same time, you can voice your concerns about the rear suspension, but 41k is pretty early for shock/strut replacement, so I doubt you will get new ones.