So I am reviewing two roms I have. One from my original tune. The other from a tuning shop. Let's say the immobilizer code is different in the two. If the later of the two (the one with different than original tune) is flashed to the car, what might happen? I had heard the car wouldn't start, but it starts fine. Does this even matter?

 

Worst that can happen is your motor goes boom!
The immobilizer must be turned off in the periphery bits of the latter, which explains why you can start it even though the code is different.