Also, End Run talks about how docked fighters are handled in ordinary transports (the ones that can't have an internal hangar bay because all their interior is used to, you know, transport stuff) - the pilot actually goes for a space walk to get into his ship then. This isn't too hard to imagine - after all, WC pilots do wear space suits all the time (well, except in the movie). Remember the ejection scenes in WC1/2? The pilots' suits are sufficient protection, basically.
(if you think about it, a pilot in WC would actually have things slightly easier in this regard than his WWII equivalent - a fighter launched from a transport in WC could dock with the transport again afterwards, while in reality, the Sea Hurricanes that some convoy ships carried actually had to fly back to an ordinary coastal base afterwards)