Since then, I've committed to only use MacOS on a Macbook and Windows on a real keyboard. That seems to preserve my muscle memory the best. But things can be rough when I use a Windows laptop or a standalone Mac keyboard.
Fixed some wrist pain I was having though from cmd-tabbing with the default layout!
With respect to Windows on the Macbook Pro, when I used Windows VMs, I would go to the VM preferences and swap the command key mappings so that I could continue using my muscle memory.
How do you usually try to press the command key? If you're going for it with anything other than your thumb, you're doing it wrong. Note that Apple keyboards often have narrower spacebars than PC keyboards, so the command key is closer to the center of the keyboard (and closer to your thumb) than the alt key on a standard PC keyboard.
I seem to be switching based on the type of keyboard I'm using. Whenever I open bootcamp I have to consciously remember to use ctrl not cmd.