My experience (mostly from about 10 years ago) has also been that
Autotools (not just how they are used) are much larger problem for
portability than the software they try to build. Autotools scripts work
only on platforms that Autotools officially support. If you have just
(GNU) make and shell like claimed above, Autotools falls down on its face,
soils itself and cries for Mama.
It was much easier just to build GNU make and re-write the build scripts
as cleaner Makefiles instead of trying to port first the huge mass of
Autotools dependencies (Perl being one of the first/larger roadblocks) and
then debug what other software the scripts need (after a long build fails)
+ iterate that.
For me the solution seems obvious. Solve the problem instead of kludging
It seems insane/impossible to try to make the scripts autotools generate
to projects portable to "everything". Why not instead reduce Autotools
script dependencies and make sure that those dependencies do everything
needed and are portable to/buildable everywhere in addition to being
standards compliant, small and of exemplary clean design?
The very small downside would be that then those couple of binaries need
to be built for given platform before the much cleaned up, debuggable,
faster, saner and otherwise better new autotools scripts can be run. But
as those programs are small & very portable, that should be trivial and
including their binaries to CYGWIN and GNU coreutils would solve this for
>90% of the developers.
As a result, all world's embedded developers would thank you!