I think this is a red herring - compiling to native code is orthogonal to low-levelness. Haskell compiles to native code, but is exceedingly high-level. Forth is traditionally bytecoded, or threaded-coded, but is excruciatingly low-level.

Java was originally bytecoded, but at some point gained various ahead-of-time native compilers. Did it become lower level when that happened? It did not.