That is interesting, as I remember one of the characters having learned their martial art from Dan Hibiki. That being said, that tidbit could have been added by the American side of Capcom.
It is strange to separate the worlds in the first place. They obviously work well together.
I assume, no matter what the previous logic was, that has to be gone now. I mean, we do have Rival Schools characters in a SFV stage.
In the first game, Sakura was a friend of Hinata, though they went to different school and she was more like a pen-pal. Then she went away.
The game always had a ton references to other Capcom games. For example, you could go to a festival with a character, and you would be asked to take a plastic mask of either Dan or Gouki. You would gain or lose affinity points depending on whether the character was serious or a goofball.
There was also a fantastic event where Tiffany would ask you to pick a costume for some occasion that would "highlight her qualities" or something. If you select anything sexy, like sexy bikini or sexy Cammy outfit, you would lose points with her. The only good answer was "a giant Sasquatch costume", which highlights her fun-loving personality, of course!
If I recall correctly, the Iinchô started learning martial arts in Seishun Nikki2 by following Dan's method (the kind of "become a master in just 6 weeks!" kind of self-help books). In the Dreamcast game, when she became playable, she had shifted to Ken Master's method by following Hinata's advice, who's also following that method. That explained why her animations were so stiff (and why she was so bad): she's sticking to the lessons of the book very rigidly, in a very close-minded way, while Hinata just take inspirations from it and makes her own style.
So yeah, it was always messy. The reason to not add Kyôsuke to Zero3 never made sense.