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The main problem with Apple keyboards is that the [Win] and [Alt] keys are reversed.
Simply press [ESC]+[W] (for Win key) to flip the keys. Done.
Note that this will only work for keyboards with an Apple vendor code. It works on mine. Open an issue if it doesn't work on yours.
If you have a PC laptop with an attached Apple keyboard, the keys on the laptop will NOT be flipped.
Cool. I want this always on
Put this in your capsicain.ini:
[config_1] OPTION FlipAltWinOnAppleKeyboards