I bought a stripped Colt barrel off the EE knowing that there was a slight flaw in the exterior. Nothing major at all, which is why Colt parkerized over it and sent it out of the factory.

The problem is that the booger is right where the low profile gas block needs to sit and so that spot needed to be sanded down so that the GB could slip over it. I'm left with a shiny spot that is invisible with the GB installed in place.

Will this ever be an issue once I get the GB pinned by ADCO?

I see no reason why you would have any problems. I wouldn't be worried about rust either unless you're submerging your gun in water. You could always pick up some cold blue just to cover it and protect the metal some. It obviously won't be a match to the parkerized finish, but won't be seen.

You should be gtg OP