Heh, yeah those are definitely problems, and I'm glad he owns up to them. The article, though, seems more like a preemptive strike against the backlash they expect to see when the next version of Firefox removes all the settings he lays out (except I doubt anyone will notice).
But that's the extreme. I still firmly believe there should be options in software, but naturally you have to be judicial in how they're implemented. To say "there shouldn't be checkboxes because they may accumulate over time into a horrible mess since we don't ever plan to audit our settings panel" seems to be a bad justification to me.
As he also observes, having plugins to enable features that don't exist in the software natively is also a good workaround...but you have to allow plugins/extensions in your product.
Anyway, that article didn't change my mind, if that's what you were going for

It just presented an example of bad implementation.