Nutplates
I would not try and cover them. Just paint. When you get back to installing screws, always use some grease and a sacrifical screw to chase out the threads filled up with a little paint. IF you have to, you can chase the threads with a tap and grease. Just be careful not to run the tap down into the nutplate too much or you will cut out the crimping on the backside of the nutplate. Then you will lose your crimping on the nutplate which keeps the screws from backing out. You'd have to use locktite then.
I use Cadmium plated screws to chase paint out of nutplates and then when I'm finally installing screws, I use stainless with grease on the threads to protect against electrolosis.......
Hope this helps.....
Aden Rich