#1: There's no reason certain players would be paid more than others. They all have the same role in the game, and would receive the same compensation. The only difference is if they are the cover athlete. Madden works the same. Brady doesn't get a bigger chunk than Fitzpatrick just because he is a star.
Even in the O'Bannon lawsuit, the players getting more money were that face of the suit, the rest get equal cuts.
#2: I severely doubt Power 5 conferences would try to get their players paid more than others. The schools have plenty to deal with and how much a video game companies pays their players is the least of their concern.
The idea for pay is a stipend, not a contract. EA sends a letter asking to use the players name and likeness for $XX dollars, same is sent to every player. The player either accepts it, or doesn't. If they don't, they're not in the game. Its what they do in Madden. They don't take the time and negotiate a contract with each player, or each school, thats too much time invested. Its a "take it or leave it" deal. That's why even in madden, every once in a great while there #51 or #17...that player didn't sign the agreement.
The old "you knew what you were getting into" idea. Many students really didn't realize it would be that difficult to make things work. They stick to the sport because they love it. Meanwhile their image, jerseys, and anything else they are on is sold for a huge profit. EA wants to pay them (and really, not even a lot) to be in the game. The amount each player would get is still almost nothing, but it could cover some meals and clothes for a little bit.