[cleszkie]

I think you would have to cut deeper into the hard top than you think to accept an uncut door. When you do cut the top, you would likely be cutting away the area where the inner and outer skins are bonded together, leaving an open gap between the skins that would need to be closed, and taking away some of the rigidity/strength of the top. It sounds like more work than its worth, and it probably wouldn't reduce leakage by any amount because most of the leakage comes from where the top meets the windshield frame above the door opening.