For me, I can explain what is loud and quiet commentary in fantasy: For instance, the violent white supremacy of the Conan the Barbarian novels is very blatant, I can see that (Robert Ervin Howard was famously white supremacist, even by the contemporary southern standards), on the other hand, the racist ideas of Tolkien's are much more subtle and harder to confront (creating the orcs after the mongols, evoking that old European fear of a mongol invasion).
I know nothing about the Conan novels but I'm pretty sure Tolkien's Orcs were originally Elves, captured and corrupted over time (so not sure how they are supposed to mirror the Mongols if they are simply corrupted versions of the 'pure' ones). Do you have a source that they were based on Mongols? I have never read that before.
I read an article recently stating that Frodo and Sam were in a closet homosexual relationship in the novels. Our contemporary cultural goggles, I think, often skew our vision as to what was intended...and obviously in many cases, shine a new light on them.