Couldn't one use ISTA-P for this? I've used it for coding alarm retrofit on my E92. I remember seeing audio retrofit in the list of items. It asks the user if anything has been changed in the car. You select what has been changed in the list of items enumerated. I would give it a try. Here's the docs for ISTA-P.
BMW ISTA/P documentation - coding / programming - BMW forum. Diagnostics, coding, programming, repair BMW vehicles.

Edit:

Read on another forum that SSS/Progman via Retrofit will also do the job.

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'05 E53 X5 4.4i, '97 E39 528, '07 E92 335i, '16 F86 X6M.