In System Preferences > Mouse there's a setting "Scroll direction: natural", which I don't like, so I unset. The problem is that this also unsets the setting for Trackpad, which I do like.
How can you have different settings for mouse and trackpad?
(In case you can't understand the rationale for wanting them different, and think this is a ridiculous question, here is the reasoning. Mice have had scroll wheels for decades, and the direction of the wheel turning has always been in sync with the motion of the scrollbar. This is, in my opinion, the most natural way to do things, even though it is the opposite of what Apple calls "natural". On the other hand, I'm perfectly willing to use Apple's "natural" scrolling for trackpads, because the metaphor here is that you're moving your fingers across a page, just as if you were using an iOS device's touchscreen. The idea that Apple treats these as the same thing, when they are conceptually completely different is very odd to me. I don't want to change a decades-old habit with the mouse, just because Apple changed their idea of how a trackpad should work. I embrace the trackpad change because it makes sense to anyone who uses an iPhone or iPad (and I use both) but I'm not willing to rewire my brain's way of using the mouse.)
Best Answer
Update 2020/12/03: As other's have pointed out, this is not a feature of Karabiner in newer versions.
It appears that this is integrated in the Karabiner app so it works out of the box without any custom XML (which are described above).
You'll need the following settings:
Set the Enable Natural Scrolling setting in the Mouse/TrackPad PrefPane to 'enabled'. This allows for the internal trackpad to work as it's supposed to. Any connected non-Apple external mouse will scroll in their own natural way.