Is this the old geezer versus the new wet diapers yet again? (trying to be as evil on both sides ;) )
There are new technologies and we should embrace them. I am not a proponent of VMs, I don't like them in general, but I do see its uses and it's very effective. Like in C++, you got STL, with very similar and nearly interchangeable std::vector, std::list, std::deque and so on (and not talking about boost or 3rd parties here). You need to know when to apply them or else you'll get problems. Well, in the '10s, you have the same ridicule amount of technologies available to sysadmins, and you need to know when to apply it. That's the new Sysadmin job, not only know that you can code one in bash with grep, awk, echo, while read, pipes and rsync, but actually know there is a package all neatly made for you, available at your fingertips with a simple apt-get (or yum).
I keep my computer tidied-up, I love to know what runs where. Even then, I do a "spring cleaning" once every year, reinstalling everything. And incredibly, my computer runs faster and more efficiently. Why? new /etc defaults, new parameters, new software, old clinging software, things that are nearly impossible to update. Same for the files. Seriously, in today's computers, we get hundred of thousands of files, most of which have some arcane use we couldn't care less, but are necessary for some kind of weird reason. I'm a sysadmin, and I don't pretend to want to know all these files.
I read the article, and yes, there are things that are changing, and seriously, I do respect the One person who can understand the Sendmail configuration files... oh I'd even be impressed with the M4. :) And when there is a problem, I want to know why, because I love to learn. But then ... there are prerogatives, time constraints, servers need to be up, people need to work, and we have all these magnificient tools that will enable every computer to be segregated in their private little VM world (to return to that main article). So should be simply shrug, laugh and go back to The Ancient Ways? You can keep you "vi" editor, leave me my "vim", please. :)