I think that is
extremely likely, and autoconf is an excellent example. autoconf hate is almost nonsensical when you realize what it replaced (though, I kinda hate it, too, because it's very confusing, but definitely not more than what it replaced...). In a world of people only building for Linux (and where Linux has mostly standardized to the point where building for one is the same as building for any other), it seems needlessly complex, but in the world of Solaris, AIX, SCO, Irix, Linux, FreeBSD, OpenBSD, NetBSD, and a bunch of others, it was simply necessary. If you didn't let autoconf handle some of it, you simply had to write your own crazy shell scripts to figure things out.
I think it comes down to younger folks not having experienced the pre-Linux world of the server-side (or at least the pre-Linux domination). There was a time when there were dramatic differences between the various UNIXen, and only something like autoconf could make an Open Source project build on anything approaching a majority of them.
I think a good example of a weird characteristic of Squid is its cache_dir directory layout. By default, it'll distribute files into a directory/subdirectory/ hierarchy. This doesn't really serve a useful purpose on modern systems (it doesn't really hurt anything, either, it just looks weird to modern users), but on some UNIXes back when Squid was being built there were dramatic performance effects from having huge directories full of thousands of files.
Likewise, the whole virtual memory argument that the original article talks about is complaining about something that was intentionally added to the Squid design in order to address the horrible characteristics of several major UNIX VM implementations (even now, having a good VM layer is not something you can just assume).
I feel a little bit of unease when I see projects that do choose the "we develop for this" model. I'm not sure it is a useful feeling, but I think we probably should keep our options open. I've made cross-platform a religion for most of my developer life, and it is perhaps less important now...but I don't think it's wise to just say, "OK, it runs on the latest Linux kernel. Fuck it, let's ship it. Screw everybody using anything else."