From what I remember when something similar was brought up a long time ago (matching transporter effect to the ship you're flying) the devs said that the transporter effect (and I assume the other stuff like scanning etc.) is baked into the character on creation depending on their faction, and that making it alterable…
That's really one of the sticking points with the system for me. Until now we've had no real reason beyond the sentimental (or wanting to do crazy things like all Miranda STFs!) to keep any of the lower tier ship in our roster so we're stuck using mostly T5/T6 ships. What would be a nice gesture is if, when the system goes…
When I first read that Romulans were not going to have access to T5 allied ships my initial reaction was "WTH?". But then after I thought about for a bit it actually made sense. If as a Romulan you had access to all Romulan ships plus all allied ships, from a gamers perspective there would never be a reason to roll…