The Minelayer’s main body still has the same topology. Maybe it could have different geometry on the top side, maybe these side turret bases might be elongated to the engines and the turret base to engine box edge wouldn’t have to be there at all. Maybe the turret base doesn’t have to be there at all, since its whole purpose is to support the turrets. Maybe you could remove the side wings or shape them differently.
The EMP might not need the side turret bases either.
Basically it all boils down to this: Not be affraid about UVs and not limit yourself to just adding additional mesh modules. What would you do if you allowed yourself to turn off the texture, go back to gray for a moment and forget UVs exist. And just be free to remodel section of the ship fresh.
If you take Vaygr Corvettes as examples. Sure, they have the same/similar engine sections and similar body. But a Missile Corvette isn’t just a regular Corvette with polygons deleted and two long missile boxes just slapped onto the model. The transition is modelled.
The Command Corvette, double sized bridge and “wings”. Again, not just imported parts of new mesh somehow wedged into a good old Corvette, someone actually took the time to make it an original ship.
This is what I meant.