1) The fact that we don’t pasken like one shittah of the Gr”a in Chukas Aku”m does not mean we can’t pasken like him in another; in fact, that’s precisely what we do. They are two different things.
2) The Igros Moshe does not say that the Gr”a on Shavuos trees argues on the R”ma; he says he argues on the Maharsha”m. Again, they are two different things.