The glass does not travel forward as much is I implied in my diagram and should clear the window mechanism and motor. With both pieces of glass out of the car it will not be hard to make a cardboard template to test the theory. It will come down to millimeters for clearance near the front, but I think the front glass corner can be shaved a tiny bit so it won't hit the door front. The triangular sidelight sits on a narrow shelf which needs to be cut out for a full glass panel to pass through. To return back to stock, that shelf would need to be replaced.
A cheap way out is to leave the existing big window in place and make the triangular window easier to remove. If needed, you can then plug in the small window on the fly.
I hope other will chime in with ideas and concerns.
Tom