Scotty,
Don't know about the 41 folder's use, as I don't have one in my version of the game and I presume that you are going to have to get that answer from the GWX team. Is there a zon file in your 41 folder? (I'm guessing that there isn't.) If there is no zon file in the 41 folder, then the stuff in there would be for eye candy and, perhaps, for increased realism for things that were not hard coded to a globally applied file.
The parts of the data you were modifying in the cfg file is just for the in-game stats, like in the library. The eqp file tells the game when 'options' become available for the player; the ones you can buy with renown. Some things can be 'pointed to' in other files, like the menu_1024_768.ini file, so additional folders are needed to keep modifications straight.
By the way, just for clarity, when I say that I play a 'stock game' it's the same game level as what you call 'patched'.
Bob
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