1: I already reported this as a bug, and was told:
It will also be helpful for you to submit a report on the Star Trek Online forum to support the details I will be providing them. {link} Posting this on the forum is also a good way for other players to pitch in their ideas and experiences.
So I'm being obedient.
2: When I was doing the Endeavor (three patrol missions in Romulan space), the NPCs gave me dialogue that clearly indicated they saw the "Federation" flag, but not the "Romulan" one:
"I'll admit I've had my doubts about working with your people. But perhaps we don't have to be enemies."
"Cooperating with Starfleet still feels strange. In time, however, perhaps this will be commonplace."
(I admit, I have a smooth-forehead Romulan, but she's in a T'Liss! Is her alternate-timeline accent that close to a Vulcan's?)
My Fed-aligned Liberated Borg Romulan got the same lines as the pure Romulan (who I think is a Delta recruit).
I have not yet tried these missions on my Fed-Aligned Jem'Hadar or KDF-aligned Reman...
3: In one of them, when I was taking a long time to kill all the enemies (I think it was in the Archer system patrol? The one with Tholians...), Enterprise showed up to help! Shon did not show up to help my Borglet, whose ship is much better than the T'Liss, so I guess it's tied to how long it takes to take out the first couple of waves rather than Shon being a kill-stealing glory-hound. (Has anyone ever had Tiaru show up in the Republic flagship? Presumably that's who should do so... I have got to try this on my Reman when it's not 3am and see if I can kill things slowly enough to make a NPC ship help.)
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Heck, Delta Quadrant even has a few lines that change depending on if you're a Liberated Borg. And then there's Captain Killy's changing commentary based on if you're Fed, KDF, or Jem'Hadar. Early Federation missions include different dialogue for Vulcans and Andorians, with the Undine faux-Ambassador. The game's code definitely has flags for both faction (Fed/KDF) and species (Romulan/Jem'Hadar/Liberated Borg).
It is entirely possible that the missions are old enough that no one updated them... But I don't recall seeing Federation-oriented dialogue back when I first took my LibBorg Rom through those as Mivek's dailies. I am very suspicious -- especially because of getting both Federation and Romulan dialogue for the same game-event -- that something in one of the updates has borked the flag-detecting code a little, so it's latching onto the primary one (Fed/KDF) and not the species one (Romulan).
The game can and does acknowledge you as a Republic character in certain instances after you complete the Romulan storyline, though. For example, there is "The Temporal Front," where you are tasked to first talk to all of the representatives of your government, and then to escort the the lead representative of said government to the conference room. In both cases, your Romulan character will interact with Republic delegation, not that of the allies that you chose.
What you're saying here is only true when no faction-specific dialogue was written for the mini-factions, which happens in a great many cases, including the Tau Dewa patrols, but is not as universal as you are making it out to be.