Basically, Autotools is really stable software that has a ton of bugfixes in it. You can't just throw that knowledge away. The overhead of unnecessary tests is negligible compared to compilation costs for anything but the most trivial project. And, I'm pretty sure if you ask the mailing list, there's a way to turn off unnecessary checks for a Fortran compiler, probably by specifying the languages to support with AC_LANG or something.

Yeah, it's clunky and obtuse, but it works to give you portability to just about every system, POSIX or not. And the free support is first class if you ever have a problem.