Not that I expect this to be implemented, but theoretically shouldn't the birds be taking off within a round or two of dropping off the troops? That's an awful big and expensive target to be sitting on the ground in the middle of a fire zone for an extended period of time?
Personally, I'd like the idea of having gunners on the transport that could provide support fire while the troops debarked and then force the transport to take off by the third or 4th round regardless of whether the troops were fully debarked or not. I'd also like the transport to be targetable and damageable by the Aliens.
All that's probably a little more hardcore then what the Dev's are interested in however.
Alternatively, if these really are clandestine, low intensity missions.... shouldn't the troops be getting dropped off some safe distance away...and enter the mission zone on foot? Maybe enter the mission Xcom2 style?
I know that's probably not as popular a choice as having the transport on the map, but thematically it might make more sense for covert style missions.