Essentially there is a sort of timeline shenanigans going on, alongside the two different worlds.
Timeline A is basically the original as viewed by someone from that world in our world(the person behind the games creation)
Timeline B is the current Elrise situation. Which as events change in isekai Elrise world, the person behind the games creation memory changes human world.
If memory serves correctly, it essentially works like this:
Timeline A Otaku reincarnated into Timeline A Elrise and becomes evil fake saint(I may be wrong, but Timeline A Elrise may have Otaku A memories)(Otaku is a person with selfish principles). Observer A reverse isekais into Otakus world.
Observer A changes Otakus world timeline into Timeline B by creating the game.
Otaku B consumes the game and loves it. And thus when Otaku B starts dying and reincarnated into Elrise B, those memories of the game influence how he would act as Elrise B.
Because time is different between the worlds, Elrise B can communicate with Otaku B as the timeline changes due to Elrise B. Information is updated as a result of the timeline changes by Observer B.
I don't really know if I accurately described things, it's been a few years since I finished the story. But simply understand that everything will be explained in a way that brings everything together and makes full sense. I was legitimately shocked at how perfect the writing of the series ended up being, and was not expecting things to wrap up so neatly.