Shadowrun's License is also one of those victims of being sliced up a lot on what seems like a permanent basis. Sorta like how the Marvel Movie rights are (or were, Disney for the first AAA corp, if you don't count Unilever or the old GE or East India companies?) held by lots of different groups, the rights to make SR tabletop games are held by a different company than the one that has the rights to make videogames and in fact apparently the reason Shadowrun Returns never had coop was because the rights to a multiplayer SR game were not held by Harebrained Schemes.
This actually isn't remotely uncommon actually. Licensing is generally done on a product to product basis, and often times not even then. Disney didn't give FuncoPop the exclusive rights to collectible Star Wars merch for example, and licenses out its tabletop games to FFG, its videogames to EA, and has multiple deals with many companies for many products, from food to Star Wars brand toothbrushes.
But those companies don't get to own any aspect of Star Wars and can't sell off the license. For SR it seems weirder because the license for the videogames (at least multiplayer ones), from what I can tell, is held by Microsoft, meaning they get to sell off the ability to make videogames on some level (as they seem to have done with Cliffhanger) even as Topps gets to sell off its tabletop rights, as well as the rights for things like novels.
The relationship between Topps, Pegasus, and CGL is not known in specific but from what I understand CGL sublicenses out to Pegasus. The reasons why are not 100% clear, but Germany is apparently big on Shadowrun so it could just be a big enough market that three different entities taking cash for the license there still works out, with Pegasus paying comparatively a lot for the license but still making off very well because the German market is just that good, while CGL gets both to avoid having to localize for that market which saves money and gets paid by Pegasus.
What especially makes this more complicated is that CGL is a LLC, as is Topps (as its owned by an LLC in whole). This means that a lot of information that normally goes public isn't really public at all, for example CGL doesn't generally publish sales figures because it doesn't need to as it has no shareholders who legally need that information. So a lot of these deals are less back room and more just not public because no non-company figures have any technical need to know. So its a lot of speculation besides the overt legal status of the products, and even that can get hazy at times.