Autotools generate a Makefile project, and nothing but a Makefile project. All the buiding in the development cycle is done by typing "make". Autotools projects include a template makefile: Makefile.am. Make is not concealed in any way.

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.