hi mike,
i must admit that i've never used the feature... and my tweaks to scribus are simple enough that i can redo them on each machine (and version of scribus) where i need them :-)
well, you got it: the best way to avoid having to tweak scribus too much to fit your needs is to write good bug reports and feature requests and hope that somebody picks it up, ping the right people until they have fixed it, or learn how to program it yourself...
i have not tried it, but i think that a workaround would be to use the exported preferences file and put it in the place where scribus is looking for preferences on your system (it depends on the OS: for linux it's ~/.scribus) and setting it's name correctly to replace the default preferences.
but you're welcome to submit a feature request (i would say even a bug, since the feature really seems only half baked...) on
http://bugs.scribus.netciao
a.l.e