If players can fly a ship that's not in the original game, they are using a player-side mod. Period. There is no way that a server-side mod can give players the ability to fly a given ship. It just doesn't work. Why? Because a bunch of values that are necessary for player-flyable ships are missing from most of the ships that only the AI flies in Vanilla FL.
I dunno why you keep insisting that somehow there's a magical solution for this- there isn't. If you try to do this with just a server-side mod, then it will be, at best, very buggy, because there will be conflicts between the server-side and player-side data.
Server-side mods can do a few things, like determine what Loadouts are being used, what Commodities/Weapons/Equipment/Ships are for sale, etc. But, when you're naming Archetypes and calling out their Types, Explosions, Fuses, Cameras (many of these things are either not defined for the AI-only ships, or aren't defined correctly), Nanobots/Shield Batteries, etc... it
just doesn't work right. This data is determined on the client side. FL is kind've funny this way- instead of having the server send a big download stream to clients, updating their INIs wherever things don't match... in many cases, FL lets the clients determine what values to use, and the server then interprets this, or crashes
So... what I've been saying here, in more and more detail, is that
I don't care if you think you saw this done because what you saw won't work right no matter what. You can make the AI fly around in the ships you never see fly in regular FL, like the Battleships, etc.- but if you want players to do the same, then they need to download a mod that lets them do this.
I don't know why this is bothering you so much- if you want to have players download and install your mod before playing on your server... big deal, it's what everybody running a mod that adds new ships (including the FL ships you normally cannot fly) has to do. If you want to see a good example of how to put the FL ships into a mod, check out my XML Toolkit Mod, 1.2, which has very nice, well-commented example code which will teach you how to do this sort of thing...