I used to take granules from the gutter and do the same thing when sealing the nailheads. You should see my new roof that he and I installed.
His solution is to seal it with roofing bull and then to take two pieces of the scrap shingles and rub them together over the spot until the minerals cover the spot completely making it disappear and blend right in with roof. Calls it unprofessional and lazy, but then his butt is tighter than even mine. My brother was a professional roofer for many years and he hates it when he sees it. I point it out on the report as a minor item that can develop into a major if left unresolved. I’ll have to find the photo but I have one where on the top the roof it shows a small hole where the nail used to be but from the bottom inside the attic you can see a tiny spot of daylight through the hole, and then around the hole for about two feet in all directions, wood rot and mold, including the rafters.
