I'm dropping a note about this here, there's an issue when you have multiple FL mods installed at the same time (I know for sure NT and Disco have this issue, I don't know of any other mods that ditched flmm yet).
Essentially, Freelancer create save files in the My Games FL folder and one of them contains data specific to the mod it's launching. As an example, If you launch Neo Terra and then try to launch Disco, you will instantly crash to desktop as soon as you launch the game. Same goes for any other mod that ditched flmm.
In order to fix this issue, the NT Launcher automatically delete the save files prior to starting the game, so you will never get that CTD anymore when starting Neo Terra. Problem solved.
The thing is, I only work on Neo Terra and I don't really have a say in what other mod devs do so it's completely up to them to fix this issue for their own players. I can't force them to do it.