Since i'm guessing you don't have idrive in your car, you would have had the BMW professional/Business head unit + some sort of bluetooth capability?
If you had bluetooth capability before you installed the pioneer head unit, you need to know that the bluetooth is not controlled from the BMW factory head unit. There is another module in the car that controls the bluetooth/multi media and it is stored in your boot under the trunk liner. These are the MULF and Combox (you probably had an MULF). If you have BMW Assist, you may also have a TCU in your trunk in addition to the MULF.
This would connected via fibre optic connection directly to your factory head unit. Think of this as the BMWs remote amp turn-on. Now if you did not remove this after you installed your Pioneer head unit, my thoughts are that this module is always staying on, because if the fibre optic connection is broken, all multi media functionality will cease to operate correctly, if not, at all.
Now because you have tested your aftermarket amp and checked that is turning off, and the fact that when you revert your entire setup back to stock, that you dont have this problem - i think this may be the cause of your drain. I say this because the MULF has the "brains" to stay on after the car is turned off. For example, if your making a call through the car's bluetooth and the call is still active when you turn the car off, the call will not disconnect and the head unit and MULF module will remain on until your call is disconnected
So if you had bluetooth from factory, all im saying is - pull the thing out, you don't need it anyway with your new setup. Plus weight reduction bro