The Star Trek universe has always been reinterpreted over time...
You're absolutely right about this, I don't think there's much room to argue the point. When I was young, there was the show and the movies, already extant, so the young mind just naturally thinks of them both as being "the way it is." But now that I'm an adult, and a bit more fanatical, I can imagine what I would've felt like seeing early production stills of TMP and wondering what they were doing to my show. And then, after long years of struggling to finally accept that, it would happen all over again with TWoK. And TNG, and every other show. But having grown with it, I do think of it as one single cohesive universe, complete with a bunch of fanatical explanations for why some things don't make much sense (like, maybe the uniform changes were because of a new Chief of Staff of Starfleet).
So, you're right that no amount of visual restylising indicates conclusively that STXI took place in a different timeline. However, and this is just from watching the movie once when it came out, but my perception was there wasn't an absolute certainty that it was the Prime universe, before Nero came back. Spock came back after things had already changed for 25 years, right? So he wouldn't have noticed if things had already been different before then. Thus, my opinion of the subject is that whether the timeline shown is the Kelvin scene is the Prime timeline or not, is one of those things that can just be left to the individual. In my personal continuity, ENT was in a timeline created by the Borg and Ent-E going back in time in FC, and then the Kelvin scene was a part of that timeline. I don't think there's anything in the movie that specifically indicates that
couldn't be the case, but if, in your personal continuity, the Kelvin scene takes place in the Prime universe, I'm not say you're wrong either. It's kinda like the question of whether the TOS stories took place in order of airdate, production order, or some people even say stardate. The Official Chronology may say something on the subject, but canon's only what's onscreen, so it's just a personal choice. I think saying that they took place in production order makes a lot more sense, but that doesn't mean that someone's wrong if they say airdate. It's just personal preference.
So, since the Concordance is a fan-created work, the fan that's creating it should be welcome to their own interpretation. Of course, such a decision should probably be up to Bjo, rather than CRA, but I'm just saying... It's not an official publication, so they don't necessarily need to stay in line with stuff that has just been implied offscreen. Of course, it would probably be a sound marketing decision to do so.
A simpler solution may just be to give a special notation to information that came from the movie, thereby allowing each reader to make their own interpretations. Best of both worlds.