Not the only grey tile on the map, and I’d rather not sacrifice a whole color to the explored-checker. I’d suggest it’s worth Marking it on your map when done.
Do you mean leaving a note to say “looted” or whatever? That’s what I used to do (and still do for stashes and whatnot), though I found it made the map more difficult to read after a while with notes strewn all over it. I like the ‘mark as explored’ feature as it’s a bit faster and less intrusive, but yeah - now that you mention it, the other grey map tiles have led to a bit of confusion too.
Maybe there’s some way it can be tweaked, I don’t know.