Very good article, thank you. I'm so glad I'm using Arch Linux (GNU/Linux)
BSD is absolutely not what it says in this article, hence the editorialized "apparently" in this article. (Hope the HN mods don't ban me for it :P)
Don't take everything on HN at face value. Sometimes things are meant to be analyzed, like that "What 4chan thinks of HN" post.
Otherwise you do it the same way, typically with the GNU build system.
The ports tree is the most natural form of package management I've used. Then, if you prefer binaries, you have pkgng and the pkg_install utility. This is for FreeBSD, at least.
Even though I like BSD systems I must admit I think Linux is a better choice on the Desktop, I would't know about servers. The most annoying thing that happens to me constantly in Linux and even as I type this is that from one release to the other hardware that used to work stops working. But this is not a show stopper as most issues can be easily worked around. Since virtualization became a viable choice to most consumers I don't see an excuse not to use Linux.