I don't know what GNU/Linux you're using, because in my experience, most packages going into a distro use make.
Oh, and then there is that whole denominator in the GNU/Linux fraction that's built with GNU Make.
Maybe you don't see Makefiles because you're relying on binary packages?
no, they use autotools or cmake, which happens to generate makefiles. the package authors themselves definitely don't write any makefiles by hand except maybe for trivial packages (and frankly I'm not sure)
Also note that not all Autotools-based projects use Automake. Using only Autoconf, with a hand-maintained Makefile, is a thing.
The goal of Autotools is to produce a software distribution that doesn't require the end user to have Autotools. The end user has a shell to run the configure script, and that's it. If that works, they run "make".
About the most sophisticated generation the user will see is that some Makefile.in template is passed through sed to substitute @@XYZ@@ variables.
And coming back to Autotools, some of the largest Autotools projects (see the GNOME ecosystem) has been moving/moved to Meson, which can also be used to generate Ninja rules instead of Makefiles.
CMake Generators: https://cmake.org/cmake/help/latest/manual/cmake-generators.... Meson: https://mesonbuild.com/ Bazel: https://bazel.build/
GNOME and Meson: https://wiki.gnome.org/Initiatives/GnomeGoals/MesonPorting
That's what all build systems do. Hell, cmake's description is "cross-platform Makefile generator".
The rationale is quite obvious: the DAG part is solved problem. The hard part is extracting platform-dependent info, perform validations, and use it to generate the DAG.
And a Makefile is a DAG.