When you enable “Override window manager shortcuts” in the keys prefs, it overrides -ALL- window manager shortcut keys, not just the ones used by Renoise.
I remember this used to work differently before. Example: i have ctrl+alt+left/right in my window manager to switch desktops. In Renoise, i disabled these shortcuts. If i am ON the desktop with the renoise window in focus, these shortcuts no longer work. Though, if i am switching ACROSS the desktop, ie. passing by the desktop where renoise is, without releasing ctrl+alt, then it works.
Like i said, this worked differently before, i think in 2.8, where window manager keys that weren’t used by Renoise weren’t overridden.