I have no affiliation with the Underground, but I voted in favor of them separating. I feel like their purpose here in the Kathol Outback has been achieved, and that to be tied down here would only mean they are just absorbed into the major faction. I've seen a lot subfactions, and most of them are just forgetten underneath the major. Not saying that it couldn't work, if it could work anywhere, it'd be here, but I don't think we should cage up the Underground and instead let it spread it wings to other parts of the galaxy.
There is no saying that there is an official separation. There are those who were formally part of the underground that decided to stay in the Outback, feeling that leaving would destabilize the region again, and so they peacefully wish the Underground well on their mission as they move forward. There doesn't have to be a falling out, the TKO Redux can certainly support the Underground cause even if its only superficial, they will just have different ideas and goals.