I've been running my '22 2dr Badlands, with stock tires for 51K miles and the noise, considering the top is 3 pieces and the door windows are frameless isn't too bad. Obviously can't compare to a solid body and framed window door vehicle.
I have the TRMR roof rack on my 2dr Badlands. I can still take out the 2 front panels. Right now I have a RTT - ikamper 3.0 mini, and a 95L ROAM box on top.
Your title is misleading. I thought you meant the rear window in the hardtop, but the rear door windows. The hardtop glass is the same. The doors are a different size. The 2dr doors/ windows are longer than the 4dr doors/ windows.
Find another shop. Mine were easy peasy. I think they disconnected the battery so the windows wouldn't lower. I paid $200 for mine - I have a 2dr. San Diego