Scrollbars are hidden by default if OSX detects a Magic mouse/trackpad but there's nothing stopping anyone from changing that to always shown (or always hidden!), as well as the scroll direction.
Maybe the solution is a prompt for a decision the first time OSX starts up, at the same time as the user is creating their account?
add a prompt you say?
do you think anyone actually reads prompts? or do they just dismiss them as quickly as possible, since they're in the way of the actual task?
Apple certainly took it upon themselves to cause the problem. What's your proposed solution?