Producing a different configuration for every system is not the whole point of autotools. Rather, autotools is generally used as a way to configure semi-standard-but-implementation-specific functionality across different platforms, such as locating <stat.h> or determining the platform's word size.
It also gives users a familiar way to optionally enable features at build time, such as choosing between MySQL and PostgreSQL support, as opposed to requiring the user to edit some Makefiles and twiddle some #define's manually.
Not that I'm defending autoconf (I dislike it a lot), but
POSIX is also ignorant sometimes, so it shouldn't be treated dogmatically - e.g., google for the socklen_t confusion.
Other than that, the real world isn't black and white either. Although many unixen claim to be POSIX compliant, based on my experience they are mostly POSIX-ish.
And there's also no guarantee for sizeof(size_t) being a platform's word size.
It also gives users a familiar way to optionally enable features at build time, such as choosing between MySQL and PostgreSQL support, as opposed to requiring the user to edit some Makefiles and twiddle some #define's manually.