Wait until you drill the VS-1008, since you will be enlarging the hole to #30. If the mark still shows, buff and dab with primer when you prime the VS-1008. A spot of primer there won't show as it is covered by the doubler.
Edit: Looking at the photo again, did you already drill #30? Without the doubler (because with the doubler in place, that mark wouldn't occur)? Either way, basic advice still applies.
Edit again: Just checked the CD plans. Page 602 still says revision 1 but the date is different than my kit, which was 2/2/06. So I'm guessing the VS-1008 now comes pre-drilled to 1/8" and the earlier instructions to drill the caps to #40 before match-drilling the doubler and hinge brackets to #30 are obsolete. My mistake.