Between you, BlackHayate02, and Aspirety, you guys wrap up the final holes in the simulation argument, yep. Sakura, Sakuya, Kotarou's appearance, two Kagaris have all been accounted for by now, making the simulation argument completely possible.
Seems like it really does become a grab bag of just picking one of the three theories you outlined earlier. All of them have proof in the visual novel, either straightforward or implied, it's just that some of the theories are simpler or more plausible. It's not that any of the theories are wrong, it's that we don't know which one is the "correct" or "cannon" one.
And yeah, I agree about Rewrite's depth. The other Key works are all pretty straight forward. Even their endings that can be baffling are mostly explained by "dat's the power of love for ya," yet in Rewrite it's about a bajillion times more complicated than that. I really like Rewrite for it.
Also, it's sad that the Sakuya scene at the end of Terra was changed. I don't know the changes, and while I was confused as to how Sakuya could talk to Kotarou at the time (you cleared it up nicely), I really liked the scene as one last bro to bro moment between Sakuya and Kotarou, showing that they'd transcended being rivals and moved on to being friends.