It's absolutely true that ".PHONY" looks like a hack; it was sort of meant to. In general you shouldn't be using it, except maybe as a facade layer where you can put an "API" (c.f. the "all" or "clean" targets) on top of things that are themselves proper dependencies.

I'm not going to hold up make as the ultimate expression of a dependency-based build system. But I will say that history has a LONG trail of products that tried to replace it with decidedly mixed results. Categorical statements like yours tend to trigger my "code smell" layer, most of the time attempts to replace make produce worse results.