If his replacement build system lets me a) build varnish under SUA on a version of windows that didn't even exist when he wrote the project b) cross-compile varnish for arm, then I'll agree with him. The "standard" gnu autoconf layout, for all its m4 insanity, gets you both those, and none of the various wheel-reinventions I've seen do.
Yes they're a pain in the ass, but a necessary one.
`uname -s` obviously doesn't cater for the divergences and bugs within a platform.
Have a look at gnulib for things one has to deal with.
BTW, one can just use gnulib and forget about lots of portability issues