Use Major Faction as bonus Minor Faction

you mean something like a fragmented world that lost the communication to his homeplanet or something like a abandoned world with few residents?

No I mean if Major faction are not add in the game you do, add them as a simple minor faction

For example, you do a party with all unless the Lumeris. When you do the game, you can find the homeplanet of the lumeris and the Lumeris as a Minor faction (with bonus like +100% dust in system for example)

Sounds like a good Idea, but it is not necessary. I don't think it will be greenlighted. 

But in the case I'm wrong I'll give it an upvote!.

This is a great idea!

For an explination, Just say that these factions are not as developed as the others, making them "Minor Factions" because they dont have advanced enough space travel from system to system.