Actually I like your "original storage scheme" better.
It's what I do, myself.
I don't trust ANY application (iPhoto, Photos, Aperture, etc.) to "manage" my photo library.
I keep my "masters" (i.e., untouched originals) in a simple finder "folder/file" hierarchy on an external volume.
I then have my image viewing/editing apps access this storage in "referenced" mode (i.e., the apps DO NOT copy the originals into their libraries).
Now I can access my "master library" from ANY image app I choose, knowing that the masters will always be there.
Aside:
I do the same with music. Even though I have many gigabytes of mp3's, my "iTunes folder" is..... empty.