I think Tolkien's direct rebuttals of allegorical content were intended to deny that the books, LOTR especially, were allegories of the Second World War. At the time of press, this accusation was prevalent; Sauron and Saruman as Hitler and Mussolini was particularly popular. I don't believe he ever denied the books having ANY allegorical meaning. For instance the theme of vanishing, ravaged and destroyed countryside was a direct broadside at the industrialisation of England's once green and pleasant land.
There are other themes, hidden in plain sight, that are allegorical in nature; your point is right in that the books were never truly intended as a political commentary in the vein of, say, Orwell's "1984". Tolkien's experiences in WW1 doubtless affected the battles of LOTR, and the central battles are reminiscent of some of the larger conflicts of that War, but I do not think the books in any way are intended as a reference to those events.
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And all the rest is literature
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