It's nicknamed the autohell tools for a reason.
It's neat but most of its functionality is completely useless to most people. The autotools are so old I think they even predate Linux itself, so it's designed for portability between UNIXes of the time, so it checks the compiler's capabilities and supported features and tries to find paths. That also wildly predate package managers, so they were the official way to install things so there was also a need to make sure to check for dependencies, find dependencies, and all that stuff. Nowadays you might as well just want to write a PKGBUILD if you want to install it, or a Dockerfile. Just no need to check for 99% of the stuff the autotools check. Everything it checks for has probably been standard compiler features for at least the last decade, and the package manager can ensure you have the build dependencies present.
Ultimately you eventually end up generating a Makefile via M4 macros through that whole process, so the Makefiles that get generated look as good as any other generated Makefiles from the likes of CMake and Meson. So you might as well just go for your hand written Makefile, and use a better tool when it's time to generate a Makefile.
(If only c++ build systems caught up to Golang lol)
At least it's not node_modules