I wouldn't pay for the transmission fluid flush, or even have the dealership do it. Start your argument with the proper TSB's and other examples of PUMA cases on this thread that have had the mechatronics units switched out. I was under CPO and a PUMA case was opened on the matter for me. I know others out of warranty who have had goodwill repairs, only having to pay for the labor for the repair.
The fact is that BMW is aware of this issue, so you'll just need to get the dealership on board with opening a PUMA case in your honor.
I see your also from Atlanta. Where are you getting serviced at? Mine was done at United BMW in Roswell.