TapNoiseIf Command and Option feel reversed on an external keyboard, use macOS Modifier Keys settings rather than relearning every shortcut. Check the selected keyboard carefully before changing a mapping.
Change one keyboard’s modifiers
Open System Settings › Keyboard › Keyboard Shortcuts › Modifier Keys. Select the external keyboard if a device selector appears, then assign the actions you want to its modifier keys.
The setting changes what a key does, not the symbol printed on its cap. Write down the original values if the current setup is customised, and keep the built-in keyboard available while testing.
Verify familiar actions
In TextEdit, select a harmless word and test Copy, Paste and Undo. Then test an Option-based navigation action. This catches an accidental swap more clearly than trying a complicated editor binding first.
Check your editor’s own keymap if only one app behaves oddly. A global modifier change can make that app’s custom mapping harder to understand if both layers are changed together.
Undo the change cleanly
Use Restore Defaults in Modifier Keys to return the selected keyboard to the standard mapping. If the old setup was custom, restore the recorded values instead.
Keyboard sounds do not change modifier meanings. TapNoise’s optional shortcut sheet reads the current app’s menus, while macOS controls this hardware mapping. For a key that generates the wrong punctuation rather than the wrong shortcut, inspect the input source instead.
Source: Apple: change modifier key behaviour.