The dealers can do it for used stage kits so I don't see why they couldn't do a used stock pcm. You mentioned Flight Systems and I know they do all of the new stage pcms and they also do used ones, too.
According to post #3 on this thread they will do stock pcms, too.
Need your pcm reflashed with your vin?? - SRT Forums - SRT4, SRT6, SRT8, SRT10 & Dodge Forum