Macos – Remap command key in mac only for emacs

(setq mac-command-modifier 'alt) ;; Can be set to  meta, alt, super, or hyper

I'm not sure how your windows keys map, but you can evaluate that expression in a scratch buffer with C-x C-e until you find modifier you like and then copy it to your init.el or .emacs file.

Aside from the "Modifier Keys" System Preferences section, I don't think an application can override the behaviour of the caps lock key..

I'm fairly sure the Caps Lock key event is not passed to applications, nor can they override the toggle effect.. Maybe you could do something whereby you monitor caps lock key state, and send alt when it changes.. but this is extremely convoluted, and slightly useless (it wouldn't work if you hold the key..)

Do you really need the caps lock key in other applications?

If so, perhaps you could write an AppleScript to toggle the Caps Lock key mapping? For example, in pseudo-code:

loop forever:
    if frontmost application == "Aquaemacs":
        keys.capslock = "Meta"
    else:
        keys.capslock = "Default

Shouldn't be difficult using AppleScript, the code from this Apple support thread should be a good start:

tell application "System Preferences"
    activate
    set current pane to pane "com.apple.preference.keyboard"
end tell

tell application "System Events"

    tell application process "System Preferences"
        get properties

        click button "Modifier Keys..." of tab group 1 of window "Keyboard & Mouse"
        tell sheet 1 of window "Keyboard & Mouse"
            click pop up button 1
            click menu item "No Action" of menu 1 of pop up button 1
            delay 3
            click button "OK"
        end tell
    end tell
end tell