Heh. I knew that was you!!! MWHAAA! Oh yes, he sees the physical similarity -- that's there at least twice in the story. He does get flummoxed by the similarity, especially since he can then pretty accurately imagine what Mary looks like with her clothes on minus the catkins and pollen but you know ewwwww generally. He even wonders if Mary might have a birthmark like the knot in the Dryad's trunk -- but he'd NEVER ask such an impertinent thing (compare Lucy). He just doesn't remember the Dryad's NAME even though she was tackling him periodically for years. When she wasn't with Susan, of course....

And really, the whole point of it was a fandom poke (and to screw with Edmund's paranoia). Immaturity. We Haz It.