I love role playing, and was testing some stuff for my upcoming game (yes, i am weird). Before the Machine Age DLC (I think, havn´t played since Astral Planes released) if you made a custom empire, and used same species name and traits for another empire with Lost Colony, they would be linked in Game creation, and back then you could create mutliple Lost Colonies, all linked to their parent and done.
Now every Lost Colony empire works only with one parent i.e. if you create mutiple same Lost Colony Empires, everyone will create their own parent empire. Idk if this is wanted or a bug.

I also found out, if you use a Cybernetic Portrait the Lost Colony Empire will not link with a created Parent Empire and just create it´s own one in Galaxy creation.

I play unmodded.

tl;dr
The Lost Colony Origin seems to be broken since the Machine Age DLC