I like the idea of a starship transporter. But it would have to make sense within the logic of your story. For example, why could you fit the transporter ship with transwarp but not the smaller ships?
I would stay away from the super-ship concept though. The idea of the best armed starship in the fleet is an old cliche and probably limits your story-telling opportunities. Cargo ships aren't usually heavily armed and it would be much more interesting to follow the story of a ship which may get outgunned instead of one that can easily best any enemy it encounters.