Here is where I cut mine at. I would cut it where it can be put back together easier and where I would be away from any hard to fix areas. I would never do a transom from the back side and cut the hull skin from the outside. I think it is easier to cut the rear part of the liner out than to take the entire liner out of the boat. My floors were good so I just cut and removed the back section. If I had to replace the floors and do stringer work I would remove the whole liner from the hull.
It is hard to see the green sharpie line in the photo but it is forward of the rear seats and turns down the face of them. This way I don't have to cut the floor or into the top of the seat either.