Robert (MPandC) does use epoxy paint on patches, and uses a flat tip drill bit to remove the paint in plug welds.
It can't hurt to paint them, but when you think about it, will panels rust thru in your lifetime if left uncoated? Maybe if you drive the truck thru a vat of acid.
It's a personal preference, IMO. I have brushed on some epoxy in areas that will be concealed in my work, which is a lot less trouble than setting up to spray it. That's another trick I picked up from Robert.
