I think it covers at least two timelines, if not more. You have the one where Mother's influence shaped the course of history and ultimately doomed humanity, and the second one where the protag is a hopeless drunk getting all these visions of the doomed timeline (or having the most insane daydreams). Their world was doomed from the very beginning, but the protag's world still has some hope, so long as the protag writes his stories or somesuch.
There's definitely at least two timelines, probably three, maybe four (and presumably more)
The main three in my opinion are:
Mostly normal real life timeline, flesh interfaces pop up here and there as people are exposed to LSD/LSD analogs. People are influenced and try to increase MHE's hold on reality (or do so indirectly by trying to use the flesh interfaces for their own purposes)
Once MHE has sufficient influence the nephilim timeline emerges leading to humans who can perceive the 4th dimension. That was what the whole witch-in-the-woods videogame was about. They weren't reacting to the game, they were selecting a future where they made the right decision. This is the timeline with the hygiene beds where the woman just leads the narrator('s PoV) to
the middle of nowhere to wait for a better timeline to emerge
Then the final timeline is the better timeline, where
MHE is just a story because the narrator saved himself from a future where he brought MHE into power
The chitinous cruciforms could be from an alternate reality, an alternate timeline, or they could just be aliens from another planet/moon in the galaxy/universe that MHE is also trying to use in case humanity doesn't work out. I lean towards just aliens personally but we don't get a ton of info about them so I'm open to changing my mind about what they are
So maybe there's just a single primary timeline where the events described all occur, but there's definitely a second one
where none of it did
I don't want to spoil S;G but that's the closest comparison in my opinion. The protagonist is the sole observer that's able to witness changes in the timeline, and as a result of that they can make conscious decisions to try and create a better timeline, but only one timeline ever exists, the previous timeline ceases to exist once the new one is selected/created and only the observer has knowledge of the previous one(s)
If you haven't played or at least watched Steins;Gate go check it out, it's the best piece of time travel/timeline shenanigan media to exist in my opinion. The remake just came out on steam (sorry for shilling lol, it's just a legitimately great piece of media)
Edit: spoiler marks for the bros who haven't finished MHE yet