The tip of that size lead is pretty(consistantly) sharp. It shaves the paint out. I think you could over a clear coat in that it would literally shave out a small line in the paint. You may have to reapply the clear after though to seal the lead in. I was able to color rivets the size of a pin tip with it using a magnifying glass, on the A-10's gear with no error.
Hard to say, dubix88, without testing it. When I get home tonight I'll try it out on a finished F-15 that has 1 coat clear gloss 2 coats clear dull and let you know.
I tried using a sharpened #2 pencil to scribe my panel lines on the F-15 but the roundness of the tip caused the pencil to slip too much causing unwanted errors that were hard to get out. I found that the skinny lead of a 0.5mm was more forgiving so I'll give it a shot and hope for the best.