Thanks @b5.belgie , great ideas to try.
After your post I started by trying the "Native Trackpad" preview feature first, just to see what happens there. I notice that the timeline now scrolls horizontally with the Magic Mouse if I do a vertical scroll gesture with my finger, so that's an improvement. It used to respond to horizontal scrolling, matching the on-screen layout direction in a way that made sense. I am not actually 100% sure if changing this setting is what made this work, or whether I had simply never tried scrolling vertically over the timeline. Either way, it used to make sense and now doesn't.
Secondly, I tried switching the Native Trackpad preview feature off, and it will not switch off. The checkbox can be deselected, but when I hit Apply then Restart, the checkbox is reselected when Fusion360 reopens. The same happens if I press OK instead of Apply, then manually restart Fusion360. It always comes back with Native Trackpad switched back on. So that def seems like a bug. Not the end of the world in the short term, because for design work I mostly rely on my 3DConnexion SpaceMouse Pro for navigating in 3D space with my other hand, so my Magic Mouse is really just used for clicking and scrolling in places like the Timeline and Browser.
In summary - at least one bug there (Native Trackpad mode can't deactivate), but possibly two bugs as my original issue remains unresolved. Would love to hear from someone at Autodesk.
Josh