Seemingly you can compile the bytecode into native during some installation of application, without loosing the cross-platform-issue.
Installation doesn't necessarily means a GUI installation. That can optionally be just a silence process that happens on the first running of the executable. (With or without a graphical process bar)
That would be (I think) much easier for the developers of the languages, and result in a faster executable, without loosing the adaptations to the current machine.