The only way it will mess it up is if you don't let it fully cure and then try to use real large bit . Then it sort of flings around like saltwater taffy and you have totally jacked up your floor. Ask me how I know...
You could go halfway and attach your bottom plates and then just epoxy right up to them, then finish studding out the walls when the floor is complete. That way you still have freedom of movement and the whole space is open but the plate won't have to go over the top of the epoxy.
It really depends, in my humble opinion, on what this space is supposed to be in its end state. If you are trying to make a beautiful floor for vehicle display or hanging out, be advised that framing walls after the floor is in is almost guaranteed to scar it up. You will get some marks in it no matter how careful you try to be. If it is just a working shop and the floor is going to take a lot of abuse anyway, frame after the fact.