It's dawned on me that one of the biggest themes of this fic may be the importance of being able to notice flaws in one's models of other people.

Not that the theme isn't present, but I almost consider that a general theme of fiction. Romeo and Juliet is enabled by the authorities on both sides not having accurate models of their respective scions. Of Mice and Men is about Lenny's inaccuracy in his model of George. Die Hard always ends because the villain does not have an accurate model of John McClane. I'm sure you could write a whole book about Death Note. etc.

While it is present in HPMoR, it doesn't strike me as especially significant any more so than other fiction, compared to the many more overtly rationalist themes already present.