Placing a felt pad on the bolt head is good advice, silicone, or some type of vinyl cap would work too, or perhaps I should just leave one of the helmet bags in the tour pack. Thanks for the advice.
I lightly sanded the scratches on the helmet (white) with 600 grit automotive sandpaper and tried several paint options. The manufacturer's customer service would not provide a paint code, but did recommend using finger nail polish (which color would have been a crap shoot).
My bike is white, but the HD white touch-up paint was too yellow. Then I tried White Out and that was too silver. Then I used One Shot which was the closest color match. I sanded that out flat and then polished with Flitz. Now I can see only one small defect the size of a grain of sand.
Lesson learned.