Red alert warnings are still voiced by the Federation computer voice (ala Majel Barrett), as opposed to something Romulan. I nominate the voice for Subcommander Mivek (the lady who you gives you Romulan mark missions in the Tau Dewa sector block I think) to do the VO for a true Romulan faction red alert system. She's very stern and official sounding.
While in Federation space, when switching sector blocks, my Romulan BOffs are displayed with the Federation bridge background. Haven't tried Klingon space yet, but I imagine that a similar effect occurs there.
I changed the costumes on some of my BOffs to give them Romulan Republic uniforms, but going to the character select screen, my captain was flanked by a bunch of Hiven clones, instead of my full BOff set. It stayed that way with multiple relogs and when I restarted the game later on. Clearing my away team set, relogging, and putting them back again seemed to fix it, but it was weird seeing clones.
[FED allegiance] Default NPC non-away team BOffs contacts are now random FED BOffs, as opposed to Rom characters as before. (I don't have any FED BOffs on this ROM character.)