If I understand it correctly, when a user pays they get all of the features available at that time. So there could be users with only feature 1, and users with

If I understand it correctly, when a user pays they get all of the features available at that time. So there could be users with only feature 1, and users with features 1, 2 and 3, but never a user who only had feature 3. That reduces the number of combinations from O(2^n) to at most O(n), and you could keep track of which older features no one has, or offer periodic free/discounted updates to reduce the amount of different versions out there.