You are right, it only works if you do it on a large enough scale that everyone is involved. Dartmouth football trying to negotiate a CBA would do nothing for anyone, including those players.
Something is going to have to give somewhere. There are definitely Title IX conflicts with a pro model. The issue is there are too many conflicting things that are piling up that something has to change somewhere. One thing I've heard proposed is that college football would have schools essentially license their branding to the pros. Effectively, college football would no longer be under the purview of college athletics departments, but would just be school branded/sponsored.
If that happens, it probably means the death of a lot of other sports at these big schools. It's why there needs to be serious sit down discussions with people in power to determine what is the best course of action for all parties and how do we best get there. It is a very complex problem and the potential solutions have a lot of potential repercussions.