By the fact that there were readers guides and appendixes, etc, gives credence to the fact that the man was brilliant IMO, regardless of how good/bad the story was. The structure was put together well enough to warrant the publications.
There are 2 heads to this dog as i see it: internal and external.
The internal visualization, and inspired creativity that results in some from reading the works can, and does, lead to many things that i think JRRT would be complimented by. But, because this is internal, there can be no objectivity. That is why I pretty darned sure that no matter how good it is (PJ's included), there will be no film made ever that will really capture how I feel the ME universe would be like, and how the story is relayed to me. Any work of art ever created is interpreted. If there were a way, there would be a "Caveman's guide to cave art for Neanderthal dummies" made and distributed. I bet that would have sold a lot too...
The external: This to me is an "after the fact" argument. Yes, JRRT would be highly dismayed. Most, if not all but the purely academic stuff, would have probably had a pack of lawyers all over it if the man was around. It was an evolving work all the way to the end, as I see it. But at that point, the door to the vision was shut utterly, and all we can do is pour over the notes and scribbles and argue this and that and intent. The finite time that there could be Answers had reached its end long before I could do anything about it anyways. At that point, there is nothing but interpretation. We can't ask the creator ..
So, my answer to the original question is: No it doesnt matter, really. But I can admit to what I dont know, and tell you I am unsure about this or that. I can definately argue my interpretation!!