Maybe "natural" scroll direction vs the old scroll-bar orientation.

Yes exactly.

I've seen this mention between comments and the article, but there is such an option! Or am I thinking of something else? If you go to "System Preferences" > Mouse > unclick "Scroll Direction: Natural". Am I missing something?

Unless they've changed it really recently you can't have a mouse scroll "unnaturally" and a trackpad "naturally". They're tied together for some reason. You need a 3rd party utility to it.

But when you change one, the other changes :(

Oh never notice that, thanks for the update