Good info, Kirby. especially for me an Aperture newbie. Scott Bourne (http://creativelive.com/courses/
) recommends against using referenced files/library saying there is more control of where your images are if in the Aperture library (wish I could remember all of his suggestion!).
I haven't come across anything that can't be done with referenced Masters which can be done with managed Masters. This is something that seems to be thoroughly thought-out and implemented in Aperture 3. It is very easy to go from referenced Masters to managed Masters. The disadvantage of going the other way is that you are doing one bulk operation, whereas if you make file storage decisions on each import you can take advantage of a custom file storage scheme.
Keep aware that with Aperture you are creating two separate storage structures: a file storage structure (for files on your HD), and an image storage structure (for images in the Aperture Library). For the file storage, you use file naming and Finder folders; for image storage you use all the internal database tools of Aperture: Projects, Albums, Smart Albums, Folders, Labels, Ratings, Version Names, etc. etc.
If you use managed Masters, you don't need to worry about the file storage structure (and can concentrate on using the database).