A quick update on what happened.
Got the car back with the new AGM battery, the (possibly not required) reprogramming done and the sat radio removed from the vehicle order. Total cost was about $600, within the range that other folks have paid for the switch to AGM.
I'm continuing the discussion with BavPro about the suspicious claim by the dealer that the Sat Radio module had to be upgraded. Specifically, I want to find out if there is any way to verify the claim from a source other than the dealer service dept.
Thanks for all the input, and I'm definitely going to check out the coding path to avoid things like this in future.