The lore that exists in the Star Control games is pretty convoluted due to the various splittings of copyrights in the series.
It kind of reminds me of some of the Man-Kzin Wars books where Larry Niven has a "Known Space" universe with many others having written Man-Kzin war books and own, presumably the copyrights for their own works.
I don't know if Larry Niven ever got into talking about canon in those books.
As far as we're concerned, we look at it like this: Star Control is a series of science fiction games and Star Control 1/2 take place in one universe which we call the Ur-Quan universe and Star Control 3 takes place in a separate universe which we call the Kessari universe and Origins takes place in a third universe (Origins).
The idea, at least back in 2013 and what not, was that you would see Star Control games that licensed the IP of various universes. So picture a Star Control game that uses the Babylon 5 IP or another with the Farscape IP. That was the thinking at the time.
We hope to get back to that plan someday in the future once we have our engine ported. Things got a little side-tracked with Covid (limited console dev kits don't mix well with everyone working from home).