"With the application handling updates, like Windows versions of Firefox and Chrome do, then that gives you a lot of control."
Of course. But the article doesn't cover privately controlled installations but how to cope with app store based updates.
Since they ran into a problem on Linux, it would have been interesting to know how the Windows or OS X app stores handle this.
Or maybe the article was misleading in that it is actually not about Linux being more difficult to handle but app store based application updates vs. privatly controlled ones.
In this case it would be strange that the two different approaches were not described for the same platform.
One has to wonder if the author's intent was to simply bash Linux by using a tightly vendor controlled installation on the other platforms and a store controlled installation on Linux, making the latter more complex to handle.
Of course this would be absurd but I've seen similar things way to often to completely rule it out.