Something you have to get used to when it comes to large scale fiction series in general is the presence of plot holes and retcons. For instance, with Sonic they were originally marketing Mania as a split in the timeline after Generations in which Classic Sonic type games could continue indefinitely. More recently now that they're taking lore more seriously, they've merged it back into the main timeline through a retcon. Other large scale series worked on by many different people over the course of decades have similar issues. Even stories largely written by one person aren't perfect and are bound to get the occasional plot hole and retcons will be necessary for the current story being told to be the most satisfying it can be. The fact of the matter is that earlier parts of a franchise tend to not be made with the long term in mind, they're telling the story that the writers want to tell right now, and that can be inconvenient for the writing of later stories. Plot holes are bound to happen and retcons are a necessary part of smoothing over earlier problems with the writing and keeping everything generally consistent in the present tense.
The point I'm getting at is that Sonic really isn't special in regards to the games not being written for the purpose of just telling a story at the time and not worrying too much about how it will fit in to future entries. Franchises grow and evolve and get ironed out over the course of their life span, so fretting about every little detail that doesn't make sense is just needless worrying. They're currently faced with the impossible task of making everything fit together, but they don't need to do a perfect job of it. All they need to do is establish the vague sense of continuity with the occasional retcon here and there to smooth over plotholes and general audiences will be satisfied. We all know it is just fiction, so it doesn't have to be perfect. It just has to be fun. The alternative would be to reboot the entire franchise so that everything could be completely rewritten into one perfectly cohesive storyline, but really that wouldn't be worth the time, money, and effort when most people will be perfectly fine with the patch job they're doing here. We might expect some lore changes here and there in future re-releases of old games similar to the Sonic Generations script rewrite, but nothing so drastic as a full reboot.