We are not talking about all verses in the multiverse, only a subsection of them. In this subsection there is a binary choice. Either Mark sides with his father and subjugates the earth, or he doesn't. Both occur the same amount of times, which is an infinite amount of times.
If you wanted to talk about the total amount of multiverses then the number would be unfathomably small, but still equal because we would still ultimately be talking about a binary choice.
So the filter tree (don't know what else to call it) would look a bit like this, with each tier getting more focused:
1. All possible combinations of atoms in the universe have their own verse
2. All verses that were hospitable to life
3. All verses where the sol system formed with an Earth
4. All verses where humans & viltrumites evolved
5. All verses where Nolan went to earth and had Mark
6. All verses where Mark got powers
7a. All verses where Mark sided with his father to subjugate Earth
7b. All verses where Mark did not side with his father
We are only talking about step 7. Now, obviously, you could fill in 1000's of more steps if you wanted, but it wouldn't change that we are only talking about a single choice.