It's also a matter of what people are willing to pay for. Even (or perhaps especially) in commercially supported software, cleanups only happen if there is a strong business case for the cleanups. And if the cost of buying an extra build machine to run long complicated configure scripts is significantly less than the engineer time to re-engineer a new autoconf system from scratch, in many companies (and certainly most starupts) --- it won't happen.
The OP cares very much about code quality as a good and important thing in and of itself. But that view isn't shared by many business people, or by many programmers in general, for better or for worse. Some have argued that OSS code tends to actually be _better_ about code cleanliness, because it's public, and people do care about making sure that their code is clean. (I've never seen the proprietary source code for the Oracle DB, but there are many stories out there about how horrible it is from a code cleanliness perspective.)
Also, the OP seems to care a lot of lots of extra library dependencies. The big problem here is that a lot of people don't really care if their package uses perl or python as part of their build scripts/makefiles --- or even if their package uses perl _and_ python scripts. The OP cares, but for better or for worse, most people don't. And I would wager this is likely true at most companies where programmers are paid to maintain the source tree as well!
Yes. Much of his poor experience is due to build systems.
Anyone who's developed anything can tell you how fragile and finicky build systems can be.
Since build systems are used by developers, who can deal with complexity much better than "ordinary" users, they tend to be rough around the edges.
They're also unglamorous infrastructure, so volunteers tend not to spend time on them if they're not paid. And they have a tendency to break the entire application if broken, and are often part of the "interface" of the software (since every distro who builds package X from source uses build scripts that rely on for example ./configure with particular options), so maintainers tend to take an "if it's not broke, don't fix it" attitude.
GNU projects in particular -- whose autoconf the author complains of -- have quite a bit of built-up cruft since many of them are very old, and also vital infrastructure of most FOSS OS'es.
It is important to note the distinction between FreeBSD's package system and say Debian apt. In FreeBSD I can make from source some package, and in Debian I can apt-get install a package, because the Debian packages are prebuilt it just comes over in several chunks and doesn't need to build. (yes you can pull prebuilt packages for FreeBSD too). But my point is that the packaging system of FreeBSD, as used, conflates building the packages and using the packages.
So if I write a perl script that goes through the source code and changes all the calls to fstat() to match your configuration then to build I need perl even though you do not need perl. (as an example). But to run I don't care if you have perl or not.
But lets get back to the volunteer/paid thing again. People who volunteer rarely volunteer to clean the shit out of the horse stalls, no they volunteer to ride in the races and build a new horse. So you end up with a lot of stuff around you don't want.
Sadly for operating systems, and the original rant is really operating systems, there really isn't a cathedral/bazaar model, its more of a democracy / feudalism kind of thing. Nobody 'owns' the final user experience for the OS in FreeBSD/Linux discussions.