Interesting question - I looked at different options - Automator, Applescript,"defaults write" from the Terminal, but could not find anything really convenient.
The settings are per user, and not per database. So the obvious solution would be to switch users to have two sets of settings, but that would still require quitting Aperture.
What I do right now, to have different external editor settings for two different databases, is to open a library in iPhoto, if I want Graphic Converter as external editor, and to open the library Aperture, if I want Photoshop. For different libraries can Aperture and iPhoto be open at the same time, no need to quit either of them. You could set iPhoto to save external edits in 16 bit and Aperture to save external edits in 8bit, or vice versa.
I will have to look into the iPhoto trick. I can actually open the same Library at the same time in each app?
you can open two different Aperture libraries at the same time this way, one in iPhoto, and one in Aperture. And this way you can use different settings for different libraries - different external editor, different Mail program (if they fix the Outlook-bug), different settings for 16bit Raw or not.
This will not prevent you from opening and editing all libraries in Aperture - I mostly use iPhoto, when I need to browse two Aperture libraries at the same time, when I want two external editors, and when I want to use "File > Reveal in Finder" for managed images (an added bonus ).