I'd agree that it should be down to the Captain. The sense of isolation - and hence independence - from Starfleet Command is very much a part of the flavour of this era.
Remember that one of the original inspirations for Trek was as a "Hornblower in space". In the Napoleonic era ship captains, being out of contact with the admiralty for months on end, had a lot of leeway in matters of uniform and equipment. Play that up and have NPC ships and officers do things differently...
Oh, and everyone should read some of the Hornblower (and also the Aubrey and Maturin) books for ideas. You won't reget it.
"And all I ask is a tall ship, and a star to steer her by."
"Though a cloaking device, pulsed phaser cannons
and a full load of quantum torpedoes would be quite nice too."