I think that keyboard and aliases should be together in preferences. Personally I would add the possibility to configure any key with modifiers under keyboard as it works already as instant shortcuts and I would keep the aliases only as abbreviations for typing in the command line.
If the key isn’t configured in the keyboard section, then the command line is triggered. If you want to force the command line you can specify any key for that…
It’s critical though to have a global on/off switch for the keys that trigger the command line right now. When “instant” is off, it works as usual. When it’s on, rhino looks first to see if there’s a configured shortcut.