From what I can tell, Sega tries way too hard to appeal to everyone in the fanbase, even the most vocal of fans, which ironically makes it appealing to absolutely nobody in the long run. For example, this is basically the reason we have Classic Sonic and Modern Sonic be in two separate dimensions, to appease the classic fans by saying everything after S3&K technically didn't happen.
The shipping part kind of makes a bit of sense though, especially considering the number of shipping wars that go on in the fandom, even during the production of some of these comics. In other words, it seems that Sega just can't trust the fanbase to not chimp out over who gets shipped with who anymore.