Upon using the I.S.S. prefix on your ship, the nacelles should also take on the purple glow like the NPC I.S.S. ships.
The explanation for the I.S.S. ships in Starfleet service could be that these ships are the ones captured / retrieved from battles for intelligence (there's plenty of mirror universe NPC ships making incursions into our space!). In the time of war, these ships are simply re-crewed and put into service.