This. I have been planning soft top from the beginning for this reason.
Regarding the wavy back windows, take a look at any soft top jeep on the road or for sale on-line, they are all this way. I'm not worried about it.
The 2 door seat are between the wheel wells, the 4 door rear seat is in front of the wheel wells. 2 door only fits 2 people in the back seat (and a cup holder for each which is super important around here) while the 4 door fits 3 people (with no cup holders).