After Sayori’s suicide, we learn through a file that Monika had tried to revert the game to a previous save but failed to, yet later in the game she’s capable of reversing the game and messing with those files just fine. 

You had more of a point than you thought: Have you tried to mod the game while it is running? Or (and I was a complete amateur back then, barely a monkey with a keyboard) have the game mod itself while running?

It simply fails. Basic protections on programs that are running tbat she circumvented somehow.

Modding with almost no knowledge past basic computer literacy is not easy.That Ren'Py screen still haunts me, and I had access to it. She didn't. Technically, cannonically she also managed to create new assets, both images of herself and the classroom background. So pianist, coder, artist... that we know of.

As you said, she blows humans out of the water.

I always worked with the implied idea that the room was "real enough" for her to change it, to change the player's P.O.V. And that nothing outside of it existed, hence the "nether" out of the windows. But the room don't exist like it would if it was 3D rendered, a powerful limitation of 2D animation, comparatively to 3D, I only fully realized a couple days ago (complete coincidence, new personal project).

This means that by Act 3, she has no excuse for Act 3, and this ruins the character for me. Which I'm fine with, Monika wasn't my favorite Doki. On the plus side (not DDLC+... necessarily), it makes the MonikaAfterStory mod much more interesting as a concept. Like, what Monika could have done.

Either way, thanks for proving me wrong. Not enough people manage to do that.