What messes me up when I'm working on a linux machine is not being able to do things like copy/paste text from the terminal with a hotkey combo because there is no CMD-C, and CTRL-C already has a job other than copying.
IMO apple really messed up by putting the FN key in the bottom left corner of the keyboard instead of CTRL. Those keys get swapped on every Mac I buy.
I agree on the Fn key positioning... I hate it in the corner and tend to zoom in when considering laptops for anyone just in case. I've also had weird arrow keys on the right side in a laptop keyboard where I'd hit the up arrow instead of the right shift a lot in practice... really messed up test area input.
It's the same thing when switching from a Nintendo to a Western game where the cancel/confirm buttons on the gamepads are swapped.
It may seem like a small thing, but when you have literal decades of muscle memory working against you, it's not that small.