Can I prevent an app from overriding a system default keyboard shortcut?
If the app has a menu entry for the command, yes.

System Prefs > Keyboard > Shortcuts > App Shortcuts

Add an entry for your app &amp; the menu command you want rid of.
Set the shortcut to be something useless &amp; hard to hit by mistake...
This will give you your system shortcut back.

Example from another answer of mine, showing how to remove 'Hide Finder' - https://apple.stackexchange.com/a/177138/85275