Considering Melkor's possible 'tweaking' of Elves to make orcs and Saruman's further magical Uruk Hai, it seems that a gradual Lamarckian shortening of the Hobbits by hole-building is probably the best bet. As mentioned, there are several races, like the Ents and Ungoliant's spiders, that are only give 'perhaps' explanations. I guess coming up with artificial ideas is as good as looking for the first pipeweed plant. In a world that JRRT himself never quite finished changing, maybe it's a question best left to the Tolkien family (hint, hint, Adam!).
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