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.
2002 WRX Sold
2007 WRX Sold
2007 STi totaled
2007 Foz XT sold