That's not how copyright works.
If it's an association issue, it's trademark. Stardock owns the trademark free and clear. The Star Control games exist within the Star Control multiverse because we say what is and isn't in the Star Control multiverse. If we were to say that the Star Wars universe is in Star Control universe, that would be an issue because of the trademark (consumer confusion) not because of copyright.
If you can't put A and B next to each other and get a person to agree (or disagree) that one is a copy (substantially similar) of the other then it's not a copyright question.
Most of the mistaken arguments I've seen on this dispute is the association fallacy. Trademark controls association. Not copyright.
As I understand it (though of course I may still be wrong here), consumer confusion is all about real-world associations - for example, a product that is marketed under the Star Control trademark is associated with the current owner of the mark (Stardock). You are correct in that you can slap the Star Control trademark on various products that you own and declare them part of the Star Control multiverse.
I'm not talking about real-world associations, though. I'm talking about fictional associations in a fictional universe. SCO makes references to other universes existing in addition to the Origins universe that the game is set in. Therefore we can assume that from the point of view of, say, the Captain, the Precursors, the Observers, etc. there are other universes out there, that there is, as F&P put it, a "hyper-dimensional" connection between the UQM universe and the SCO universe. That's a story issue.
So if you say that the UQM universe (which is owned by F&P) is part of the Star Control multiverse, then to an observer from the UQM universe the SCO universe also exists as a real entity. Basically, F&P must edit their story against their will because someone other than them owns the Star Control trademark? Don't copyright owners hold exclusive rights to their stories?
I realize that I've already had a similar discussion with you over half a year ago on the UQM forum, and I realize it's up to the court to decide who is right... So I'll understand if you don't want to continue this discussion.