Lately, we've seen DnD and Pathfinder move away from some of the more blatant signifiers, like renaming "race" into "species" and "ancestry," and in the case of Pathfinder, having systems in place to mix ancestries in a character build. DnD has decoupled good and evil from species, and pathfinder has done away with good and evil entirely ( keeping a vestige of it present for things like demons and angels).
Race is almost alwys tied to a language and a culture, with, say, kobolds having the same certain cultural signifiers all over the world. To an extent, this makes semse because different peoples in these games can have different physical abilities, or have different origins entirely, which would naturally lead to them developing along different lines -- If one people can breathe underwater and another was born from a volcano by a specific god's decree, that would inform how these cultures behave.
Is it possible to have a fantasy along these lines with a materialist underpinning, or is this very idea of inborn powers anathema to that sort of approach?
I think the more useful thing to do is not to hide these stereotypes, but to state and then question them. There's this passage from Lords and Ladies -
Elves can then be used as an allegory of how the aristocracy does the most horrible things one can imagine, but then surround themselves with an air of refinement.