I finally finished the update and there are some points I need clearing up:
- Why the fuck did Makoto's father randomly die at one point and never reset to being alive again, did some God kill him for no good reason or something?
Addressing some of your other questions as well, but focusing on this one because it's the easiest to explain.
Maya wished for a world where she could repeat that perfect moment in time with Akira, creating a time-loop bubble. That time loop bubble was a copy/paste of the original world, much like the quoted text above is a copy/paste from your original post.
Note how I only copy/pasted a part of your question. Everything else is gone. Does this make the quote I did copy fake? No, it's a copy, but just as "real" as your whole post.
That's what our Kumon Mi is. A copy/paste of the original world. The world is "fake" in a sense, but the people inside it are as real as their originals, though they are likely began drifting away from their "source code" almost as soon as they were created, as they are shaped by different experiences than their originals.
Makoto's father was outside the boundary when the copy/paste was done. He was never a part of our Kumon Mi, he only ever existed as a memory for those in Kumon Mi who remembered him from prior to the copy/paste wish. Since the original world was subject to linear time instead of the time loop, he's been dead for a very, very long time, as has everyone else who lived outside the bubble. Everything else is gone.
The Gods are watching Kumon Mi, because it shouldn't exist. It's an anomaly. It's
entertainment. One of the Gods thought it would be funny to call Maki and inform her that her husband was dead just to see how far this anomaly can be pushed. That same God also thought it would be funny to call Haruka and inform her that her husband was still alive, just to see how far this anomaly can be pushed.
All the other instances of divine fuckery we see (Nozomu/HOPE pushing Akira do do X by Y time or Z happens) is also all likely just the Gods prodding the anomaly to see what happens. Maya's wish created a fishbowl, and they're just tapping the glass.