Dumbledore, unlike Flamel, may not fully believe Voldemort can really use the Crown to find the Stone. Otherwise why would Dumbledore ask Flamel to remove the Stone from Hogwarts - does he really care more about the safety of a few students than about Voldemort getting the Stone? If so, he could prepare alternative traps, just on the chance he is right.

Also, whatever he believes, there's no reason for him to mark the true location of the Stone with corridors to which he directs the Gryffindor students. That just increases the chances that Voldemort will use the students to get at the Stone, or will encounter some of them while there, and harm them. Why would Dumbledore not separate the Stone's guardroom from his challenge to the students, unless he doesn't think Voldemort can locate the stone, and is using the students' forbidden corridor to lure Voldemort into a trap?