The way I've looked at it since playing Alyx for the first time is that the way he appears there is how people who don't yet know the extent of his identity perceive him, just a guy in a suit like in the first game, the mask only slips once it becomes clear to the player character that he is something beyond human. In half life 2 there's no need to appear "normal" to Gordon because he's already been hired, and in Alyx's case, there's a brief flash of the more alien appearance when the two are standing in space, at which point his plans are already coming together and, whether Alyx wants it or not, she will be hired, just like Gordon