I agree with your assertion. But the Galaxy-X is from an alternate time-line where the Klingons had defeated the Romulan Star Empire and, I'm guessing here, that Starfleet felt that the Treaty of Algernon was null and void then. In our time-line, the Romulan Star Empire is still around though they are fragmented after the super nova destroyed their home world. IMHO, the Galaxy-X shouldn't be included in the game since we are back in the "normal" time-line, based off of TNG, once the anomoly was closed and Q was satisfied. Granted we are still in an alternate time-line based off ST9 but since the Romlans are still around, the Treaty of Algernon is still valid. Just my opinion. Do with it what you will.
"The treaty reinforced and redefined the Romulan Neutral Zone, and made clear that any violations of the Zone without adequate notification, by either side, would be considered an act of war. "
So how come we aren't at war with the Romulans? We seem to be able to fly freely in to the neutral zone and further in to Romulan territory. If that is allowed then I see no point of the treaty in other aspects either.