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Your understanding is right.
When the game starts the addons are loaded and processed. Data they need from their saved variables files are loaded into memory. Changes you make to the saved variables file while in game will be overwritten when you log out as the file gets re-written with the appropriate data.
Even if you rig up the ability to import data for your addon ( like I have done ) the moment you do a reload or log out it will replace the file with the data in memory and reload it back into memory.
Now it doesn't stop you parsing the saved variables file with an external program but you would have to do it after you have logged all the way out of the game so that the correct saved variables file is processed.
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