I agree: Harry's goals are meaningful to Harry regardless of why Harry holds them (parental influence, Voldemort influence, etc.).

Understanding why these beliefs are held is useful to make sure there is sufficient evidence for the belief. For example, if Harry's "unverbalizable fear" of failure (that the sorting hat tells him about) is the fear of being separated from his mother, then Harry could take more appropriate risks by being aware of this. Harry appears biased against friendships/alliances with weaker students (such friendships are seen as threatening by a narcissistic parent) and biased toward terribly risky unilateral actions to protect relationships with parent figures (Quirrell, Hermione). Another example: someone I know who enjoyed HPMOR was nicknamed "genius" by his grade-school friends, but he left an MD/PhD program to become a high-school teacher, presumably so he could continue to be the "genius". He might have been a good researcher if he had learned how to lose, and recognized that his parents would still love him even if he wasn't always the smartest person in the room.