Yeah, I forgot how much of a pain in the arse it was. I did get lucky and start from the torrent file which was fully playable off the bat. It was only after that did I find out about everything else. It's to do with the retail data. The Source was made open years ago, but the retail data fell into a grey zone since it was perfectly legal to make copies of the game between friends and family as stated in the EULA. But the question was how far did that extend. So they picked some weird middle ground where they could give you almost everything but some select files which were mostly the FS2 mission/GFX/sound data. It's not too different in some ways to Open Transport Tycoon. Binary was free for all, but you had to extract or get your own GFX files.
Most of the GFX has been replaced with upgrades, but a lot of things still point to the retail stuff, so you still have to use it.
In terms of retail data playability, it's 100%. Now it's all mods, GFX updates and extra features that expand the gameplay. Like partial Newtonian physics allowing you to do a Babylon 5 Starfury/BSG overshoot turn and shoot behind your direction of travel. From what I hear FS will never truly do Newtonian.
There are still some old limits coded into the game based on the limitation of the hardware back then, but they are slowly being worked out. it's mostly revolves around how many live objects there can be at anyone time. Everything from ships, missiles, projectiles rocks, debris, turrets. Once you went over that limit things start to disappear, misfire, general mayhem.
There are probably a couple more things that might pop-up, but they are mostly nags, like Hi-Res HUDs, menus or something like that.