Keep it simple, this would be my preferred scheme.

preferences are constants, constants are implemented using a method  
#giveMeBigStuff ^ true

Load a MyPreferences class (at start-up if you wish) as a subclass of  
PreferencesDefault with your settings in and point

Smalltalk preferences ^ MyPreferences current

If you want domain specific preferences simply add a method

PreferencesDefault seaside ^ WAPreferences current

So usage becomes something like "Smalltalk preferences seaside port."

You can override seaside preferences by implementing MyPreferences  
seaside ^ WAPreferencesForMySite

For project locals, the project can use a local preferences accessor  
(Project current preferences) which can be pointed at a chosen  
preferences implementation.

As a final nuance, I would extend this by implementing "Preferences  
current" as a thread local variable, giving you per process control.

As a result of this email I have added a new type to InstallSeries  
*.prefs

This works the same as an update stream, except it always loads the  
last item in a *.prefs update series. Running an update at startup  
will then re-load the preferences.

thanks

Keith