My Current Framework for Making The IOPR Universe Make Sense:
(based on the theory that it was actually the space stations that disappeared from the world)
The Quiet Rapture: A God from an alternate dimension peaked into the world, and took a bunch of space stations to it's own universe, leaving behind a variety of anomalies. This created a time warp that had to be filled in with years of a false history for humans to comprehend the sudden change in their perceived reality.
Astrophage | Anomaly 1: The virus that destroyed all of the stars in the Raptureverse bled into the main world and began eating the suns there.
Backrooms | Anomaly 2: A labyrinth that formed in the location of the god breeching the main universe, and it latches onto the memories of the people inside because otherwise it is incomprehensible. Also yes, it disobeys the laws of time and space because location means something different to this God.
One Wish Willow | Anomaly 3: The alternate God accidentally ripped out a bunch of trees with it, and had to replace them with replicas, resulting in willow trees capable of defining reality.
(Room for other anomalies if someone wants to add another franchise to this universe)