[pcl]

Note that on Mac and Windows, at least, you can trivially do this remapping. I do it on all my computers.

On a Mac, the keyboard preference pane in system prefs has a "modifier keys" section, which is bizarrely separately configurable for the built-in keyboard vs. a USB keyboard on their laptops. On Linux, the configuration is different for the VT vs. window managers.

[duskwuff]

It's configurable per-keyboard because not all keyboards have modifiers laid out the same way. Mac keyboards have the bottom row ordered Ctrl, Alt, Cmd; Windows keyboards are ordered as Ctrl, Win, Alt. So, if you're using a Windows USB keyboard on an Apple laptop, you'll often want to swap Cmd (= Win) and Alt on the USB keyboard, but leave them alone on the internal one.