I'm afraid this is going to be an ongoing maintenance issue for you. The more you remove/reinstall the rear seats, the more scuffs you're gonna get, and even if you paint them, you'll constantly have to repaint them. Perhaps if you investigate epoxy paint, you'll be able to stretch the interval between touchups. Beware the paint flake residue left from removing/reinstalling your seats. If you are as retentive as you indicate, it will drive you mad.
Sheesh, and I thought I was kin to Adrian Monk......