This is nothing to do with Steam Downloader and the API, and everything to do with the publisher of the game not enabling those who don't own the game on Steam to download workshop mods. The API Steam downloader (and similar web pages and tools) uses is a web-based API - it never had anything to do with the game itself. If you want a mod that's Even though Steam sells the same game, it will never recognise that a non-Steam game you add is the same game. If you want to have Workshop install Skyrim *cough* "Fable 3" mods for you, you'll have to actually get the Steam version of the game, either by buying it, receiving it as a gift, or redeeming a Steam Key.
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