Yes, I exactly did that, with a soft cotton flat bed sheet on the hood, and thin satin sheets at both front driver and passenger doors where there were the seams of the cover touching the paint.
I was able to use a couple of black metal paper clamps at the fender lips to hold the bed sheet in place prior to covering, and at the doors, I simply rolled down the power windows, inserted the thin sheets,, then closed both windows, thus holding those thin sheets in place draped down over the doors. No ill effect on the windows and in both instances this added protection did considerably lessen the rubbing-marring.
Downside is it is an additional pain in the keester, time and work spent, but the paint and saving it from wear is worth the effort IMO if there's no other option.