I think Skaia is omniscient, so yeah it would recognize a player. It's never been shown to be immune to its own brand of "magic", though, so maybe it would fail to recognize a void player or someone otherwise veiled by Void stuff. I mean, maybe it's not immune, or maybe it's immune but it likes to/is forced to play along with it, that's another possibility. If a player is pulling a fast one, and does it competently, maybe Skaia has to pretend to be tricked by that to make the narrative better. It really depends on how you're interpreting the "behind the scenes" mechanics of the session.

(When I ran a game a few years ago, I decided the way it worked for that game would be that the Aspects were in conflict with one another and each session was a sort of roleplaying game being run by a particular aspect playing the role of Skaia. The point of these games was for that Aspect to "make an argument" for why it deserved to take up more "conceptual space" than the rest. The players and the denizens were the game pieces of the Aspects as well, but with much less power to bend the narrative. The idea in my mind was to treat the original comic's narrative as all sessions being run by the Time Aspect. It was an interesting way to look at it and very useful for deciding what the narrative bent towards and away from, what decisions certain NPCs would take, etc. All the other aspects were helping the players but fighting each other at the same time)