Most newer keyboards I know have a toggle so the CMD and ALT switch in software. I had to switch from Mac to Win and Linux so often that I simply kept my CMD key where Super or Win is located and got used to it. Still sometimes weird when I use an actual Mac keyboard.
I do this as well as swap command/option on the built in keyboards. It works great for me switching between my own computers/OSes but always a second of re-calibration when I touch someone else's Macbook.