And I will venture a guess that the first guy that came up with that genre was still low key with their approach where the protagonist, while still altering the events, is mainly bracing himself for the bad outcome while taking advantage of knowing what's going to happen and thus must keep the progression somewhat close to the original so that he can keep taking advantage of the game knowledge.
I don't know who the first one that came with this genre, but earlier works are indeed like that. Some works even have the villain juggling between "Batman" and "Joker" just to make sure everything stays in line with the original story.
And since in these stories you don't really see the villains POV other than the final confrontation, so you get the leeway of being able to do whatever you want behind the scenes as long as the main plot beats still happen.
Yep, as long as the story progresses the same, it's no problem even if the villain creates a new massive organisation as a failsafe in case the story leads to bad end (multiple ending game story)
Then everyone starts apeing the concept and now we have derivative work where it might as well be original plot because the protagonist deviated right away.
Ain't this inevitable? People will modify older resources to the point of being a completely original path, same as Thesis, in a sense. What hasn't researched? But those university students still find new things based on old papers.
What's the point of Pokémon isekai if right away Isekai Red quits being a trainer and work as a lab assistant and have nothing to do with being the very best.
In my eyes, just to make a difference. It's like a "what ifs" scenario, and as long as it's written well, people will read it for the sake of exploring new ideas. In turn, some writers might get an inspiration and further deviates the original genre. It's inevitable, and the market audience likes it.
Try to open syosetu and you will see what concept is trending right now, and try to remember it. Few years from now those trends, if they can shake the market like "isekai" back in the day, will inevitably ends up here in this site as an adaptation.