Talked to BavPro again and have a little more info.
(Note to mostroad: item 4 in your earlier post appears to be incorrect. BavPro uses ISTA, as do lots of other independent shops, which AFAIK talks directly to BMW)
They have their ISTA system back up and running, so they could do the programming there but my car is over at Weatherford....
One thing that the dealer and BavPro appear to agree on is that changing the battery type does require reprogramming the car. This is out of sync with some of the posts here, and I can't explain it. One other point is that any future need for reprogramming, like a module change, will trigger the same need to upgrade the sat radio hardware.
Assuming that the BMWNA rep is able to remove the sat radio from the vehicle order, it looks like I'm only going to be charged a few hundred for the programming, which will put the total bill in the $6-800 range, about what others have paid.