The hotkey remote was originally created to make controlling Remote Buddy with handsets from Sony Ericcson (which can/could act as Bluetooth keyboards with pre-defined button->virtual key combination map) easier. For these, using many modifier keys doesn't matter. They're only in the profile after all.

If you're using a mixture of Apple Remote and a keyboard, you might prefer to keep using your keyboard as a regular keyboard and control Remote Buddy solely with your Apple Remote.

Best regards, 
Felix Schwarz