I suppose what would be most helpful to us would be a picture showing what we are trying to visualise from a few words.
Also a bit of a goose-chase from your irrelevant info about other heads, not making it clear that it wasn't this head being described.
I would still doubt that a 1.5 thou recessed small area as I imagine from your description would be a problem for an annealed gasket to accommodate.
However, if you are determined to eliminate it, I can only see 2 ways of doing it. Assuming the rest of the surface is flat:
Build with weld and re-surface, or a fine skim biased toward the front.
As to how it happened in the first place:
Can you remember the first time this impression was present? Had you had the head off on a previous occasion when the impression wasn't present? ie. do you know that it has appeared during your ownership?
It could be a defective casting that just barely made the grade originally when surfaced.
There could be a region of porosity in that area of the casting rendering it more impressionable.(you mentioned the bolt boss was deformed).
Unlikely, clutching straws, a hard,unsoftened patch of the gasket at some time ago? which acted as an incompressible mold.
A small long term seep of combustion gas eroding the alloy.
Overheating combined with porosity might do it?
Just free ideas