I know that this is probably a little late, but when it comes to the standoffs, you're really only worried about making a good electrical path to ground for the motherboard. Where I work, we use power supply PCB's with an identical standoff/grounding system that motherboards use.
That being said, if you take the standoffs off before painting, like I do, the threads will do a decent enough job of cutting back into the metal when you rethread the standoffs into the chassis. There's nothing on the backside of where the standoffs screw into, so the paint will have a strong desire to dethread itself and "pop out the back." If you really wanted to cover them and be 100% sure, little tubes/ingots of rolled up masking tape twisted through the threaded holes will do the trick, too.
However, if you leave the standoffs in the chassis and then paint, you definitely want to cover the tops of them, or at least stick something into the threads - again, you can use a tiny ingot made of masking tape, or you could just screw the screws into the threads, and back them out after painting is done. Personally, you'd be way better off and have much less hassle using tiny pieces of masking tape to cover the top face of the standoffs.
Ideally, you don't want paint on the top of the standoffs, since that puts paint between the standoffs and the motherboard's grounding points, re: the sun-shaped ring of metal around the motherboard's mounting holes. It's not great to rely on the screw to provide the path to ground (for a variety of reasons), so you really want this surface to be clean and bare. As a precaution, I always sand the tops of my standoffs lightly even out of the box to make sure there's nothing between the standoffs and the mobo to increase resistance.
In contrast to screwing the standoffs into their chassis holes, where the paint wants to pop out the back, the threads inside the mounting standoffs have nowhere for paint to go, so at best you will jam the paint into the standoff and not be able to fully seat the screws, or it will make a barrier between the screw threads and the standoff threads. At worst, you'll have filled up the internal thread of the standoffs with primer and paint, and no longer have a threaded hole. This painting method leaves a *lot* of primer/paint/clear coat on the metal, and internal threads like to fill up with that kind of stuff, not just due to gravity, but with the threads wicking the paint from the face they're cut into.
You really want metal on metal to give the least resistive path to ground. Worst case, if you already painted over the standoffs and absolutely had to, you could hope the threads don't jam up with paint, and just sand the top surface of the standoffs to expose metal again. If they do jam up, some surgery with a map, bobby, or push pin might be in order.