So it turns out that in addition to the random gifs extracted to the gif folder, there are also models that don't belong in the folder hierarchy, as in they are not indexed in the table at the beginning of the wdb. I have a feeling that this is because these models are loaded when the game first boots up and are always loaded into memory, whereas non-essential models are loaded based on what part of the game you are on.
I think these models are the minifig models for the game. As with the other models, the extractor has had trouble extracting them, but there is definitely model data there. If I can get around to it this week I will try to update this tool with minifig support added. Here is a list of all the models not found in the wdb table that weren't extracted or even acknowledged before, in case anyone is interested: