I think there's something to be said for the idea that the Empire (and not just the Empire, but the Sith too!) of this era become the Republic/Jedi of the next era. Let's look at the next big era that we know a lot about post-TOR era. The Brotherhood of Darkness vs. the Army of Light. Now, the thing that strikes you (particularly about the Jedi Order) about the Army of Light is... they don't seem to have any similarities with the order of -this- era. They don't use the same hierarchy and structure, they have Jedi that lead armies and command their own fleets and ships. Not only that, but they use one particular title: Jedi Lord. Why, one might be mistaken for thinking that the Army of Light under Lord Hoth is... basically, Sith that follow the Jedi Code and wield the Light Side. Which is exactly what I think they are. Let's go on a little theorycrafting romp, shall we? The Empire wins this war. Not a total victory, wiping the Republic from galactic history. But I believe the Empire conquers most if not all of the known galaxy, and the Jedi and Republic flee to the fringes of space. However, this leaves things open for the Sith to do what Sith do: With the Republic and Jedi annihilated, with their victory assured and the Sith Empire ruling the galaxy, the Sith begin in-fighting for who gets to be king of the universe. The Emperor is already out of the picture, so now it becomes a battle royale amongst the Sith, with the Empire continuing as it always has. Eventually, however, a victor emerges: The Light Side Sith (you can learn about 'em during a Sith Warrior story). They ally with the remnants of the Republic and Jedi, and use that to take over the galaxy... and eventually merge the two entities together. So the Empire and Sith win, the LS Sith win the ensuing political machinations, and mix the Republic/Jedi and Empire/Sith together into one. This answers the question of Sith-styled ship designs appearing in the Republic, their use of the symbol, and most imortantly, the fact that the Army of Light era Jedi Order are basically LS Sith in their trappings. Least, that's what I'd do.