Once you glide out, you cannot get back inside Airship Beta for a long stretch of the game. The way across from Alpha and the side openings are sealed, and the door in the wrecked front will not respond. This is a wait, not a lockout. The main mission The City of Fear sends you back in, and the remaining doors open then. The Beta trophies still to come all need a gadget you do not have yet anyway, so there is no need to hunt for a way in, even if your map still marks them. Alpha stays open the whole time.