This is how work is actually done, and my mental model matches how I and my colleagues and yours as well actually work.

I could contort my mental model to make it match how Git works, but it is a contortion that some tool imposes on me.

We work in computing, I would expect everyone's mental models to be computational, not equational - different algorithms with the same result are still different. QuickSort is not the same as Merge sort just because they have the same inputs and outputs.