FWIW, the 11-12 ECU's are a bit different than the previous years. MY service guy told me there wasn't a way for them to see if the car was flashed and by what (unlike the previous years) <-- But take that with a grain of salt.
Also, if it's a Subaru approved part (spt, sti...etc...) they can't/won't void you out for tranny issues in the future (that portion).
Tell the service manager if he's going to have a tude you will plaster his name and dealership all over the interwebz.... Normally, they will back off.
Keep your head up.