Given your examples, I think you'd have fewer issues if you were working with unsigned integers exclusively. Although I'm curious about what other code you were referencing with this: "But seeing how each change both made the code easier to reason about and more correct, I couldn’t deny the evidence."
With regards to modulo, in Zig if you try to use it with a signed integer it will tell you to specify whether you want `@mod` or `@rem` semantics. In my case, I'd almost never write `x % 2`, I'd write `x & 1`. I do use unsigned division but I'd pretty much never write code that would emit the `div` instruction.
I'm not saying you're wrong though! Everyone has a different mind. If you attain higher correctness and understandability through using signed integers, that's great. I'm just saying I'm in the opposite camp.