Hi,
Yes, absolutely! In fact, you can change the command keys of most OS X applications. Go to your System Preferences and choose “Keyboard and Mouse” and select the “Keyboard Shortcuts” pane. Then click on the “+” button at the bottom, choose Scrivener as the application and then enter the exact title of the menu item whose shortcut you wish to change (e.g. “Bibliography/Citations…”). Then click into the shortcut text field and type the command you want (e.g. hit command-Y). Click “Add” (or “OK” or whatever the button is called) and you’re done.
Hope that helps.
All the best,
Keith