More I think about this more I'm wondering how it's going to be in practice. I look at say how MS Word stores config in documents as an example.
If I'm exchanging documents with another user, that user does not want to inherit my workflow and preferences they want to use their own.
I do agree it's time for a shakeup in preferences, there seems to be some functionality that appears to be in the wrong place and could be moved..
Another thing that could make life easier is to be able to import/export preferences and have multi user profiles to accomodate.