I suspect that: a) it would be an insane amount of work to get your box fitted correctly and b) if the player's ship didn't fit inside it would just move them outside of it.
I have made a shuttle mission and the first line in the description is:
"SHUTTLE MISSION: This is designed to be played using a shuttle."
I suspect that is as good as it gets right now and should be good enough. With people who aren't even going to read the first line of a mission when accepting it there isn't really anything you can do. A shuttle restriction option would be nice but in lieu of that just stating clearly it is meant for small craft should suffice.