Did anyone notice the bit about the Philosopher's Stone? I had initially assumed that the PS was following canon, and the reason that the PS remained intact in Hogwarts was that Voldemort made no attempt on it and bypassing the incredibly elaborate protectings (per book 1) prompting its destruction by Dumbledore & Flamel.

But now we have Harry suggesting it be moved, Dumbledore agreeing and it not being moved because Flamel wants it at Hogwarts. Well, in book 1 when they discovered it could not be kept safe at safest place #2 (Gringotts) they moved it to safest place #1 (Hogwarts) and when safest place #1 failed, they just destroyed it. Dumbledore breathes no word of destroying it, despite both him and Flamel consenting to it in canon.

And notice, if you check MoR carefully, at no point is Harry aware that the guarded object is the Stone; nor has Flamel been mentioned anywhere near Harry as creator of the Stone - Flamel has only come up in conversations with Dumbledore/McGonagall/Snape/Quirrel. (Although the topic is one would expect to be of keen interest to Harry: the Stone, recall, grants immortality or at least anti-aging.)

Conclusion: Eliezer has diverged from canon and carefully kept Harry ignorant because the Stone is going to play a role in future plot events. Given its properties, probably a large role - it's now a massive Chekhov's gem.

EDIT: See especially http://tvtropes.org/pmwiki/posts.php?discussion=722rasd1fu9p8mn5fdcbp572&page=89#2214