Git itself requires you be able to think of it as both models, diffs and snapshots. For example most uses of `git rebase` are clearer if your mental model while doing so are of diffs.
That only one is how it's implemented is besides the point really, until you get _quite_ low level.
Of course when working with Git it makes sense to think in changesets. But OP was specifically modelling the technical side starting with "We have files, which are inert objects …".
That only one is how it's implemented is besides the point really, until you get _quite_ low level.