Of course, I have no insight into this matter; but, I would suppose the dispute is about artistic integrity and not about money. They have enough money. But, they may think of some of their songs as belonging to a greater whole, like the white album. How many people would get Her Majesty or Revolution No. 9 on their own, or even appreciate those songs out of context.
Now for EMI, it might be about money. But, I don't think it is for the others.