Thanks for the reply!
To me, an extension is the code that performs the action(s) plus its menu entry point(s) (thus, several menu items might interact with the same pool of preferences). You might have one piece of backend code that handles multiple commands, which require a shared set of parameters, and which may come in from any number of menu options. Or you might have several such pieces of code, each handling its subset of preferences but requiring access to the others in its family.
Here, it seems that design pattern is inverted, with each menu item being the "extension" complete with a unique ID that identifies its preferences and *only* its preferences. While the backend code may be the single, shared script, the preferences would only be scoped to the ones based on the id of the menu item it is called from.
If there is a concept of a preference hierarchy here, I'm not seeing it so far.
There are ways around this, but they come at a cost: either one makes the sole entry point for a complex extension a notebook of panes and pulldowns (adding UI complexity), or one has several "extension" menu entries as entry points and manually manages the preferences file directly.
The latter assumes that the preferences file handle isn't held persistently open by Inkscape - and it's also not clear if the UI can be made to show preferred values on startup anyway, though in my specific case I just need to know their values at this point, as the gui is hidden for that "single click" functionality. This would be best managed within Inkscape though. Perhaps it's worth a feature request, though I'm not sure how amenable the devs would be to that.
I appreciate the input, and if there are other ideas I'm open to them as well.