Examples? I mean, there are some broken tools (EDA toolchains are famous for this) that generate multiple files with a single program run, which make can handle only with subtlety and care.
But actual tasks that make manages are things that are "expensive" and require checkpointing of state in some sense (if the build was cheap, no one would bother with build tooling). And the filesystem, with its monotonic date stamping of modifications, is the way we checkpoint state in almost all cases.
That's an argument that only makes sense when you state it in the abstract as you did. When it comes down to naming a real world tool or problem that has requirements that can't be solved with files, it's a much harder sell (and one not treated by most "make replacements", FWIW).