Yes the notches can vary in size [ weaver or pictinney ] as well as the screw size as you have seen. But the screw should fit down and flush with the slot....even though you may have some play from front to back.
Not to worry........the notches are to keep the base from sliding "forward" during recoil. So just keep the base with mounting screws forward inside the notches and tighten them down. Generally, all you will have is one raised mounting screw to engage the slots in the upper & this is enough to keep the base from sliding during recoil. To be more correct.....during recoil the gun is slammed backwards, but since "bodies at rest tend to stay at rest" the scope base wants to remain in place and not move with the gun......so the net effect is the base appears to have slid forward after the recoil is over. I hope that is not confusing ??
JF.