Also a Mac user for nearly 2 decades. I don't care too much about most of the things mentioned in the article but I absolutely agree with you about the new System Prefs.
I think its been this was as long as OS X has existed, maybe even earlier versions of Mac OS were the same?
For some power users, perhaps because if you don't need it, it hijacks a lot of key combinations that you could use as custom keyboard shortcuts.
I jest, but there was a time when I could find my settings in under a minute or two.