So if someone creates a new file and integrate the content of the old file to reach the same folder state than yours, you think s/he does something different?
It also happens that one is much, much more common in software development than the other, so it's a much better mental model of what SEs do.
So you're clinging to your mental model. Thanks for proving my point.
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.