Blackavaar, firstly some kudos - cheers for this spent weeks messing with uniforms and rerolling because I didn't like it when the game first came out. This gives me that peace of mind and I love using it.
Now, I've been having a think about the 25th century uniforms. With my latest character, I've decided to try and keep things as close to the in-game "feel" that Cryptic has designed, away from the older canon stuff.
Now I've got a theory about this that helps me feel more comfortable with my ship crew having a different uniform than my bridge crew.
Most of the officer NPCs you come across have different uniforms, but it seems to me, the standard officer uniform of the 25th century is the default one you start with in the character designer - Starfleet B-01. So this is what my Bridge Crew have (with correct divisional colours, not career colours though).
Now 99% of the NPCs walking around without rank insignia have the Starfleet A-01 uniform, so to me, I consider this to be the games enlisted crew uniform, not the officer uniform. They have a similar enough feel for me to go together. And this way my ship interior doesn't feel so odd.
So that's how I roleplay it, or justify it, or whatever you want to call it, in my mind.