^^^
From when I had my 93 I remember I had color underneath the coating. However, I don't think you can remove those side skirts, they are welded on. And I am also not so sure about adding M3 skirts either.
From what I have heard about most people trying to do this, when they got done, the paint underneath was no where near the other paint quality. Would require a lot of polishing and waxing.
as you already stated, the best and safest bet would be to get them painted when you get your bumpers done.