An easy way to test this is the following:
Install a mod, and have it startup as normal. Make it somethign simple, but ensure it has a SavedVariable. Then grab the lua from that add-on specific modvariables.lua file, and toss those in a SavedVariables.lua file.
I _suspect_ (but can't test at work) that the game is loading the add-on specific variables and then the SavedVariables.lua file. We have the ADDON_LOADED firing multiple times before the VARIABLES_LOADED fires, so it makes sense to me that the global SavedVariables.lua file would load after all the add-on specific variables.
It would then save out the new variables you replace in the SavedVariables.lua.
This is likely only a solution for right now-- and I can't be sure it will work in future patches. With them segmenting the SavedVariables out so much, they may soon deprecate that file (if not disable it completely).
Sorry I don't have a ton more detail (my lack of WoW at work saddens us both)
