Others have been a part of both. Tom Brady was a backup at Michigan in '97. Troy Aikman was with Oklahoma in 1985 but was injured early and missed most of the season. Cam Newton almost became the third, but he is still the only one to win the Heisman, start on a national championship team, and start in the Super Bowl.
As far as Montana being the best. If that's your opinion, that's fine. I would still take Johnny Lujack as the best ever. I would even take Joe Theismann second. I could see an argument for Montana to be next.