Maybe your indie was pissed you wouldn't have him flush the tranny - did you let him know you were bringing it to the dealer for that part of the job?

I suspect sabotage. I can't see any reason this would happen after a simple flush with new fluid. I think someone added something improper to your transmission - on purpose.

Or maybe it just failed on it's own and it's just coincidence.

This is why I first attempt to do everything myself. The less you bring the car to someone, the less they will try to find (or make) something wrong. Granted, a rear main seal replacement is beyond most shade tree mechanics.