The thing is, the series was often....inconsistent....with things like distance. At one point, Lyta implied the entire region of the B5 "known universe" was only seventy light years across; later on, it was stated the Brakiri homeworld was "100 million light years" from Babylon 5. Neither figure makes much sense. "The Rim" can mean the "rim of the galaxy" or "the rim of explored space", but I tend to go with the former. The fact there's no 1-to-1 correlation between hyperspace and realspace also makes mapping difficult.
There are other inconsistencies...the Pak'Ma'Ra are supposed to have only one world, but the Centauri were later reported to be seizing worlds on the fringes of Pak'Ma'Ra territory to create buffer zones. Hard to do that if they only have one world. Etc, etc, etc.
My opinion is that the worlds on the map are the "major" worlds, and that there are likely many more minor worlds, outposts, and so on, scattered throughout the galaxy.
One difference between something like the B5 universe and a typical game setting is that Babylon 5 was created piecemeal as needed for stories. Outside of a general "sense" of things, the universe was not created first and then stories written to take place in it. Given 20-odd pages of background and a firm idea of what the universe was like, Babylon 5 episodes started being written, with details being filled in as they came up. So "Beta Colony" was used in several contradictory ways, then it was retconned in the Psi-Corps novels to be a generic term -- there's a LOT of Beta Colonies out there. And so on.
It's important to realize JMS didn't create a universe and then decided to tell stories in it, ala Tolkein. He started with the story he wanted to tell, and built the universe to support that story. The further from the story, the less the universe was built. Now, as roleplayers, we want to tell other stories in the universe, so we have to take the hints and implications and build on them, to fill in the gaps as best we can.