the only character who would have the knowledge and incentive to magically confuse Harry about this is Quirrell himself, who seems to be incapable of directly using magic on Harry or Harry's magic

I seem to recall there being early evidence that McGonagall was influenced by Quirrell, one way or another, to ensure that he ended the school term as teacher. It seems out of character for her to knowingly enchant Harry, but I recall a line where she explicitly dismissed a felt sense of doom in a way that seemed out of character.