I guess it could have created a hot spot due to uneven deposits, but on a street car I can't see the temps getting that hot due to an uneven pad deposit. I suppose a hard spot could develop from repeated overheating in that one spot, but I'm skeptical. It may just be hard to remove the uneven deposits completely.
One possible solution would be to run a set of
"scrubber" pads to remove the deposits. I think I have a box at home--I'll check--could part with them cheap if I do. Cheaper than a set of rotors if they're still well within spec and do not have a run out issue.