"Also my footprint for my REI half dome 2 doesn't extend to the rainfly, just directly under the tent."

And it shouldn't. If you are calling an extra ground cloth a "footprint", the ground cloth needs to be just under the actual tent itself (if you are going to use an extra ground cloth at all, many don't) because if it was larger, the rainwater would run off the rain fly and pool on the ground cloth and then run under your tent, soaking everything.