As a sysadmin for about ten years, this argument makes no sense to me.
Zed has created a new, flexible configuration method using sqlite, which lets me easily automate changes to the web server configuration. If version control is an issue, I can easily automate taking a human-readable, source-controllable dump of the database however often is reasonable.
Bernstein, on the other hand, decided that everything about the UNIX system was wrong, and built his system around what he asserted was a better way. All of qmail went into /var/qmail, which meant you had to either symlink everything in place anyway or add it to your $PATH, which caused unnecessary confusion.
He encouraged a different (non-human-readable) timestamp for log files (http://cr.yp.to/libtai/tai64.html), making it a huge hassle to take a quick glance through your log files for something without piping it through at least one extra process.
While we're talking about config files, he also used one config file for every variable (allowed hosts, virtual domains, etc), meaning that checking to make sure you configured something right involved cat'ing all kinds of files back and forth and scrolling up and down in your terminal.
He designed the qmail build process to hard-code the user IDs into the binaries, meaning you couldn't move a compiled version of qmail from one server to another unless all their UIDs/GIDs were identical. He also made qmail use inode numbers as file names for messages in the mail queue, meaning you couldn't move a queue from one server to another without renumbering each file.
Finally, he prevented people from shipping modified copies of his source code, meaning that adding any new features to qmail required patches, with a very significant chance that two patches for different features would interact in unexpected or inconsistent ways. It also meant that if you didn't have the original source tree and wanted to add one single feature (or even change the UIDs qmail ran under) there was a significant chance that you would lose features and/or your config would break.
Presumably this last rule was put in place to prevent people from fixing all the brain damage that went into qmail's ridiculous design. It caused nothing but massive headaches, and linux distributions had to jump through hoops to provide qmail as a package, since one single change to the source required the installer to download, compile, and install it for you.
qmail was a system administrator's nightmare because DJB had in his head what he believed to be a much better way to manage software on a UNIX system, and he went out of his way to make his software use that and force people to deal with it if he wanted to use that software (making qmail open source for most of its lifetime). The problem is that that might well have been a great system, if everything was using it, but since no one but him used his wildly varied system it just made qmail a headache. For as long as sendmail was the only alternative, it was a headache worth dealing with, but once Postfix came along most (open-minded) sysadmins jumped ship at the first opportunity.
Qmail is horrid, non-free software, but, like Windows, it was horrid, non-free software we all had to deal with for a long time. Now there are other, better options.
So I'll reiterate: qmail was a horrible mess that made my life, as a system administrator, a huge hassle. Mongrel2 and its DB config file, on the other hand, are ideas I'm ridiculously excited about, and can't wait to put into production, because the flexibility and power available in this sort of config philosophy are things I can do a great deal with.
Don't compare Zed to DJB. DJB looked down his nose at anyone who didn't like his pure, pristine system, and if you didn't like it, too bad for you. Zed, on the other hand, has gone out of his way to make his software work with whatever workflows we, as sysadmins, need to implement. That's worth some high praise, as far as I'm concerned.