What you're seeing here is a confluence of two unintended shifts that are sort of propping each other up.
You've discovered the ALT-S data which is unfortunately both fascinating and pretty hard to square with any later continuity… or in some cases the continuity included in the box. The fact is that Wing Commander III on its own doesn't especially care when Wing Commander III happens. 2669 doesn't come up anywhere in the game itself and was in fact decided after the fact by Creative Services when they were putting together the Victory Streak manual. As much as Chris Roberts and the development team had an idea or care when the game happened, the thought was that it was about ten years after Wing Commander II: 2676. As you've noted, the interesting thing there is that from the early ship specs (which are pure lore) you can see that at least the Arrow and the Thunderbolt were in fact suppose to be around before Wing Commander II… so years of whining about what a retcon it was to have new ships that were old have always been wrong on their face. So our first behind-the-scenes shift is that Wing Commander II got kicked back about seven years in the timeline.
The second is that Wing Commander Academy was originally developed as a sort of 'Wing Commander III Babies' concept. All the way up to the very start of production the idea was that it would retcon Secret Missions 2 and instead tell that story with Wing Commander III characters as the wigmen: Cobra, Flint, Rachel, etc. Model sheets for characters and vehicles were already completed and the first episode was already being animated when the late decision was made to instead stay in continuity with Wing Commander I. But that change came too late for large portions of the first episode and as a result it aired including both Hellcats and Arrows. Two other later game ships that had model sheets finished show up in blink-and-you-miss them moments later on when scripts called for something different and they happened to be available: the Longbow and the Avenger.
So as a result, you have Hellcats, Arrows and Longbows in 2654 which isn't exactly what anyone ever entirely attended… but it's canon, in so much as that means anything. (Actually, if the Arrow in WC3 was supposed to be 16 years old it should've been around in WC1…)
I should also point out that that's ALL we know. You will hear fan stories about how the Longbow 'used to be a shuttle' or the Hellcat was really a Wildcat… those are both fun explanations but they aren't anything that has ever been published. (I'm a big fan of the Wildcat story, I think the Longbow/Avenger one is kind of stupid… they're just being used for SAR on the show like they are in the game…)