Harry's failing pretty badly to update sufficiently on available evidence. He already knows that there are a lot of aspects of magic that seemed nonsensical to him: McGonagall turning into a cat, the way broomsticks work, etc. Harry's dominant hypothesis about this is that magic was intelligently designed (by the Atlanteans?) and so he should expect magic to work the way neurotypical humans expect it to work, not the way he expects it to work.

In particular his estimate of the likelihood of a story like Flamel's is way off. Moreover, the value of additional relevant information seems extremely high to me, so he really should ask Dumbledore about it as soon as possible. Horcruxes too.

Edit: And then he learns that Dumbledore is keeping a Philosopher's Stone in Hogwarts without using it and promptly attempts a citizen's arrest on him for both child endangerment and genocide...