No, you are missing the OP's point..and he's right.
Pit an Odyssey cruiser against a Miranda.
In this battle, both ships have access to cmdr rank boff abilities in ALL their stations.
Who would win?
The odyssey of course. Why? More weapon slots. More shields. More armor. More everything except maneuverability.
Bridge officer stations should unlock as the rank of the player increases. They should all be 1 rank below the player's rank.
This allows higher level players to use lower level ships in a multitude of roles. For example the Miranda would be an excellent combat support ship because it can use subsystem attacks and deliver torpedo damage or tractor beam support. A low level science ship is much faster and turns much better than the higher tier ones..and although it has less science stations it could be a rapid response science ship.