While the MPT tune may not be causing a failure of anything and it just be a software bug, I'd be leary of just living with a check engine light because then how will you know if something else goes awry?
By no means am I implying Mike at MPT is doing anything wrong, but it somewhat bothers me that his first response is to say it isn't his tune. I would have expected he would request some datalogging to see if he can definitely rule out his software or tuning before making such a declaration. Hope you can get it straightened out since you seemed so pleased with MPT otherwise.
If the light were to stay on permanently, it would just be a matter of plugging in the SCT periodically to check wether any new codes have appeared.
Actually Mike at MPT did request a data log. I just need to get it to him. I was running the stock tune all yesterday and no codes popped up. The light went out and I couldn't coax it back on. The MPT tune is on the car again and still no light and no code. I need to wait for it to occur again before I datat log.