Through modding, you are able to make it so custom factions (or even standard factions) use a different set of ship designs for all its ships by editing the ShipClassDefs and FactionShipStyleSetDefs files.  However, you cannot package the custom ship designs with the mod because mods don't recognize a folder within the mod folder for ship designs.  

In my previous tests, if you define things in the xmls mentioned, they don't even recognize ships and designs in the My Games/GalCiv3/Designs folder.  They only recognize ones in the program files/steam..etc.  Designs folder.  

I would think no more than a couple lines of code would solve this.  And it just makes sense.  If modding is intended to be a valuable part of the game's growth, then this seems to be a no brainer to me.