I was wondering if this would be possible. Say you walk into a transport ship and the doors close the ship takes off and goes into space while you are in it. The ship lands into an enemy hangar and the doors open allowing you to get back out. Would that be possible to create this without the ship having any problems during flight?

Not really. You could place "seats" with hardpoints inside the ship, and assign these as passenger slots (and move the camera for the passengers inside the ship as well).

One of Psychofred's beta vehicles can do this. I think it is the republic command shuttle or something like that. The only problem is getting through the shields.

I've kicked this around a lot myself, I'm wondering if it's possible through LUA to do something like:

On enter region, if is character human, force into turret (passenger slot) then playanim closedoor/takeoff, you fly to the hanger, and once you enter a final region, you can get out of your chair.

Someone smart with LUA can tell me if that's possible, the reason it'd be necessary to force the human into a seat is because if you don't enter a seat, you'll fall through the back of the ship wherever it's going, and you won't be able to pass through shields etc.

Another option is to just have the passenger slots be inside the carrier, somehow get the ai landing stuff working like Mav did for dark times 2, and then you're good to go.

That's all I have, if there's any reason why the above won't work please point it out so I'm not giving bad advice.