Sigh..... this is ONE of the two options - it's called "managed". The other method of using Aperture, called "referenced" DOES NOT store all of your images in one compressed file.
This means you can access the images directly with other applications if you choose to do so (e.g. I created a whacking great panorama with PSE6 the other day using files catalogued in Aperture). It makes the limitation of one external editor to call from Aperture less of a hassle, as you can "open with.." from Finder, or any other application as well.
I suppose I should explain my workflow:
(1) Import using Aperture in referenced mode, nominating the destination folder on the disk, and the new project name that Aperture will manage them in. I apply a default copyright and attribution field to all imported images at this point
(2) Rate the images on completion of import (1-5 stars), or Reject
(3) Apply keywords - some combos of keywords for all images in a session, other images might get additional specific keywords
(4) Usually don't find myself applying the same set of adjustments to groups of photos, but if necessary change white balance etc and replicate for all the affected images
(5) Now review the images individually - crop, heal, clone, straighten, sharpen, saturate, desaturate, devignette, fix highlights and shadows, contrast etc etc within Aperture.
(6) Next step is variable - print, export to psd, tiff, jpeg or whatever with a range of options.
Sometimes I may work on it further in Photoshop (not often). Sometimes it's just close Aperture and do some other work....
Just for a party trick, I can show you the same NEF appearing open simultaneously in viewNX and Aperture and PSE6, if you like!
Regards,
Calx