What you propose would be possible, but you'd also need to alter the value of the PATH envvar every time external media was inserted (not a major issue admittedly), so that things installed to /mnt/cf/usr/bin (etc.) would be picked up.
I don't know why it's done this way (though I imagine some apps need to be in /usr/local/whatever and won't accept living elsewhere which might be one reason), perhaps a question for the openzaurus-users/devel mailing list.
Si