The term "supergroup" was always understood by me to just be a term used to drive up hype on something. As a journalist, I used it myself from time to time. I don't put much stock in it as a fan, nowadays. I mean, having Mike, Derek, and some other guys that were or are in groups that were popular (or are popular) in prog and other genres of music, is, well, going to be described as such.
I'd just ignore it, and forget about the characterization.
As for the "what happens if MM quits DT" scenario, I have two thoughts:
1. If that happened, I don't think DT would ask MP, even though that is personally what I'd want to have happen. Time heals wounds, but it seems from an outsider's perspective that MP and JP have some deep wounds that I'm not sure would heal enough to make it happen.
2. If MP DID return to Dream Theater, I think this current new band he has constructed, no matter where it is, would cease. It would be redundant, and I think everyone would realize that. At the very least, it would be turned from a band into a "project." Again, just my opinion and speculation.