The current plan involves a prisoner transfer shuttle. The docking bays can be used for different purposes (even carrying TIE fighters, I suppose) but this one, according to your information, carries six transfer shuttles strictly for moving prisoners. The shuttles can be used for other purposes, but typically a dedicated supply ship would replenish them if need be. You don't know the schedule for the supply runs, but you do know the schedule for the prisoner pickups.
It would be hard to bluff your way in using a transport shuttle. A prisoner shuttle, flying a known course and timetable, would be easier to get inside.
You could try it though, certainly up to you. But also consider that a transport shuttle will carry fewer troops, leaving you with fewer forces on board, and you need 50 people to operate the ship bare minimum, and even that is working everyone like dogs.