From last week's Reddit AMA ("Ask Me Anything") with Joel Hodgson:
“Would you be open to guesting on a Rifftrax? Finally having Joel and Mike together riffing a movie would be the ultimate love letter to fans.”
Joel_Hodgson: “I would say yes. I think it will happen when the time's right.”
So it sounds like a real possibility, and the only problem is logistics and timing. Frankly I would love to see some sort of Cinematic Titanic/Rifftrax/MST3K crossover with the 'Bots and everything, but it sounds like at the very least we can hope for a Joel/Mike team-up.
Highlights of the AMA here.