With Hotspot, hot areas of the code are compiled, lessening the virtualisation overhead.
We compile some C libraries and use them via JNA. It takes time to create the cross-compilation environment with all the correct versions of the libraries they depend on (and the libraries that those libraries depend on).
In comparison, if a library works on Java version x, we can include it and debug it running on the JVM as necessary.
The only advantage of a VM is that the actual executable artifact is platform agnostic.