But wait, in the only WC named game I played though, you actually had to be inside the bay before the mission would end. That was Prophecy, admittedly, but still, you had to actually get inside the bay before the mission over event would trigger unless it was one of those missions where if you didn't get inside, the TCS Midway was going to jump out and leave you behind if you didn't get there in time. In which case, the mission could end with you watching the Midway and any support craft she might have around jumping out.
So how do you make it work if that was the dynamic for all the Wing Commander games and not just Prophecy? Pick a point and make sure you can't get close enough without going into the bay by careful design of the models and setting of the SEXP?