I personally like the appendices and optional rules being included right there in the three books. In fact, not having a particular nostalgic attachment to the 3LBBs or their organization, I'm in favor of rearranging things to be more logical and practical. One of DD's main charms for me is that it takes the meat of the original game, which is already so dang solid, and presents it in such a clean, functional (but still flavorful) way. If I want just stream-of-conscious, I could just print out and use the 3LBBs instead. I like that DD forges its own path to a degree, while remaining faithful to the spirit and the solid bones of the original.
I don't know if that feedback is helpful or not. I thought the organization adopted in V4 was already very solid and made sense to me, so hewing closely to that wouldn't go wrong in my book.