The Skywalk has been used as an airport terminal in many commercials (and a movie/show or two), so it seems appropriate. (Anyone remember the Porter check-in that used to be here?) Having the terminal at the far end of the station also maintains most of Track 1 (Platform 3) to be used by conventional GO services, with the short ARL train set not crowding out say the Richmond Hill train which could still use Track 1 from the east (but as a long-time Georgetown Corridor commuter, I'll miss the convenience of Track 1).
Taxis can load/unload on Station Street, which makes it a very short walk (and elevator ride) to track level. There's room in those shuttered sports stores that could hold a lounge and check-in machines.
I am not a fan of the ARL for many reasons, but this set-up makes the most sense for it and its flawed business model.