This is by construction and is nicely explained by the slides I linked before.
Basically, autoconf generates a makefile which will work for your architecture. It does that via a script which is called "configure", which generates that makefile. The configure script is independent of your hardware and platform and does only require a standard POSIX shell, and it generates code for the version of "make" that is present on your platform. This means that in difference to other build systems, one does not have to install (and build!) the build system for the own platform, and also that there are no compatibility problems because the configure script always matches the source code distribution.
On top of that, the "configure" script is also automatically generated, typically using two files "config.ac" and "makefile.am", via a command which is now called "autoreconf", but this normally happens only on the developer's system.