I guess by "too transparently" I mean the following. The worst kind of author tract is when an author shoehorns in some point they want to make in a way that has nothing to do with and distracts from the rest of the story. We already know that HPMoR is about rationality and whatnot - it's exactly what it says on the tin in that respect - but nothing in the story so far suggests the later appearance of a superintelligence, and if one were to appear it would feel shoehorned in.