per unabomber's faq:
Can the dealer detect my reflashed ECU (AccessPort/EcuTek)?
YES the checksum of the ECU changes.
YES the dealer can easily read the checksum.
NO the dealer has nothing to compare the checksum against there are many revisions of the WRX ecu they all have different checksums. If the dealer had someway of putting this checksum into a database he COULD verify that the code had been modified but at this time he doesn't.
The 05+ ECU and some of the 04s have the VIN in the ECU code. The current versions of reflashed ECUs only change the tables so the VIN will report when queried.
Bottom line: If you don't want modifications to be detected, don't modify the car.
i'm pretty sure that applies to opensource as well. from this, it seems there really is no possible way for the dealership to tell without pulling the rom. even if they do, they have nothing to compare it to. so i guess the answer is no? they can't tell.