The entry for "Multimedia: Play/Pause" you've already found is specifically for dedicated multimedia keys.
There is also an entry "Playback: Play/Pause" to which could assign the Ctrl+5 shortcut.
Because the multimedia keys have their own entry these are the only commands that can have two different keyboard shortcuts.
i went in hotkeys, and in "multimedia: play/pause" ctrl+5, and set it as global.
if i do that the multimedia key play/pause will not work
the problem is that i need both this hotkey beacause i have a notebook, so when i'm with the notebook i use the numpad for control musicbee, but i use the mediakey when i'm with the keyboard