Unix was fragmented long before 1991, when autoconf was created. Prior to autoconf, Perl's Metaconfig did this dance, and a lot of other, lower quality systems like imake were used to work around the problem. The forces behind Unix's fragmentation was actually not the Bazaar (open source software), but attempts by multiple parties to independently build their own Cathedrals (in attempts to differentiate/provide value with proprietary systems). Of course, autoconf, as a GNU system, was, in Cathedral & Bazaar terms, a Cathedral, not a Bazaar.
Autoconf is ugly/copy-paste code because it is comparatively rarely run, so as long as it produces a passable result, people use it and focus their efforts on other, bigger itches.
There's also a long history of open source products which have enjoyed higher quality implementations than their proprietary equivalent. The Apache project itself stood as a higher quality web server than a lot of other choices (not as true today, but it was true for quite some time).
One could go on...