My best guess as to the reason you can't do it in dynasty but can in RTG is simply volume (a single player vs the possibility of many players). But again, this is a guess as I am not a lawyer, but as I have mentioned before in other posts, if people don't think that EA hasn't thought about this or attempted to come up with a solution pre-launch, then that is very shortsighted. There are two different questions here - why isn't it in the game, and can it be patched. I would have to imagine that the answer to the second question is absolutely yes, it could be patched, IF there were ever a solution to the legal issues surrounding.
And the reason they are able to do it for Madden is EA has an agreement with the NFLPA which represents all players - there is no such organization for NCAA football players. Each school has jurisdiction over their own decision to be represented in the game (there were talks a year ago that Notre Dame hadn't even decided to be in the game), as does each player. This is similar to why Bill Belichick has never been in Madden, because he has never signed off on it - there is representative group for coaches like there are for players, thus each are responsible for granting their own rights.