Yeah maybe it's less visible nowadays, but in the past the world was not just Linux and FreeBSD. There were many commercial Unixes which differed from each other and from Linux. And to be portable to such systems you needed to check everything. So autoconf was a crucial tool, not just a fancy noop.
I lived in that world, sunos, solaris, unicos, hpux, aix, irix, ultrix. I always found it preferable to have Os and even compiler specific includes for a whatever definitions needs to be different. and I certainly wasn't interested in having a rewrite pass on the makefiles. but it worked well enough when I dug up something on archie.
and then they wrapped it another layer of translation, and then another and I think more. and things started breaking because I needed the right version of autotools, and at some point I started just running "cc *.c -I. -o foo" before even starting to try to use configure, and it usually worked and saved me a lot of screwing around.
its certainly settled down some, but only because everything is really linux. but still we're here more than 30 years later checking for socklen_t.
it was a always a bad plan.