What’s more, the changes to the information on which this “baked in” build logic is based is not tracked very precisely.

kbuild handles this on top of Make by having each target depend on a dummy file that gets updated when e.g. the CFLAGS change. It also treats Make a lot more like Ninja (e.g. avoiding putting the entire build graph into every Make process) -- I'd be interested to see how it compares.