Are they though? The "complex .d-file generation" is "gcc -MMD" and a "-include *.d" at the end of the Makefile. You specify the dependencies, and it's on you to get those right, as it is in every other build system. I've never seen a race condition.
The problem with Make, is that it works just well-enough to allow people to sorta get it to work without requiring them to learn how to actually use the thing. Then they don't read the manual, and complain that Make doesn't, in fact, work.
Nice job, you just hit a footgun: try to remove any .h file (and the corresponding #include directive) and see your build just break. You need an empty `%.h: ;` directive for make to ignore missing .h files.
Make is full of this stuff and as a distro packager having to deal with each's individual quirks is prone to drive one insane. Please consider using meson, at least.
I do not believe that adding such rules for ignoring files is wise.
I prefer to just run "make clean" after I delete, rename or move source files.
With a properly written "Makefile" nothing else needs to be done and there will never be a broken build. With a properly written "Makefile" nothing has to be done when adding source files.
The problem with Make, is that it works just well-enough to allow people to sorta get it to work without requiring them to learn how to actually use the thing. Then they don't read the manual, and complain that Make doesn't, in fact, work.