For custom empires, if you want to be able to choose the Minor faction that will begin on your home system, currently you can do it.
If you want to choose each MF that will appear in the galaxy, indeed you can create a mod: the bigger part will be for the GUI in the custom faction screen but it's possible :)

I think the idea was more to be able to use a Minor Faction as a Custom Faction itself, rather than being limited to the Major Factions. I'd be interested if this is possible, I'd also be interested if it's possible to simulate the Endless Legend behaviour of assimilation - That is to say assimilating a minor faction grants you access to their ship designs.