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.
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.
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.
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.