THEORY TIME!

Sega of Japan/Sonic Team does not care about the story beyond the outline. There is little if any quality control on the actual scripts themselves.

My belief in it is just how much they care about the quality control in art. Delaying comics at the last moment because they do not bother reading the script and only notice things being bad when the art shows it being bad.

We have seen them demand changes in the art in rereleases this is one example (another is the way Metal Sonic's barrier worked that was mentioned on Evan Stanley's patreon I will show it if necessary).

I am genuinely convinced that the scripts may not even be translated into Japanese.