You can always leave the bar in the rear window, whether you roll it up or take it right off.

although the zippers are a pain to start on the new jeep, i think they were much worse on my last jeep. It was so bad that for the last 3 years i always rolled the window up, and left it attached when i folded the top down.

It didn't scratch the window even though it was coated in dust (a short part of my daily commute is on a gravel road), but the top was an aftermarket by bestop, so i don't know if the plastic window material was better than the stuff that jeep used for OEM. I would always wash the jeep when the dust got too bad on the window (or if it was caked in mud)

i have only rolled the window up once with the new jeep, i usually take it right off instead.