Ok, people, we've got some good news all around.
First of all, I am happy to say that I was mistaken. After discussing with a programmer at Phoenix Interactive (the modding team behind the Stargate, Mass Effect and Halo mods), it appears that I misunderstood Gearbox plans for future updates, and the current 3D files ingame will not be made obsolete in a game-crashing way. That means the cool capital ships from Wing Commander Saga are here to stay, and most likely future-proofed!
The other good news is that since Phoenix Interactive released a demo with campaign missions and their main programmer was cool enough to give me some advice over Skype, I've been able to use their template to start programming single-player content. I want you people to understand that the status of this work is unreleaseable due to a major lack of support assets like soundbyte integration, music, etc., BUT, and this is a really big but, what is currently working, and I tested it five minutes ago, is a completely scripted mission, here the first mission of Wing Commander IV:
You have a pair of individual named fighters. As soon as they get close enough from Orlando Depot, they get attacked by a flight of Razor. Then, after dispatching the pirates and getting in close proximity to the depot, Seether arrives, nukes the Depot and jumps out. The player can then go to Bluepoint, where the fighters will automatically land as soon as they get close enough. Once the fighters landed, a shuttle takes off, and the player can send it to a jump buoy, where it will automatically jump out, ending the mission. It's a lot of scripts and macgyvering, but it works, which means that more complicated mission structures can be set up from now on. Also, what would be nice and immersive would be to play the relevant soundbytes from the game when each scene happens.
The less than good news is that we are having some weird issue with some of the new 3D files, which sadly cannot be easily solved, so we are trying to find out what mess them up in order to add the next Border Worlds and Black Lance units to the game. In any case, though, I'll try and see if I can start working on some single-player missions based in the Wing Commander III timeline, for which we have all the required assets.