Let me summarize:
Emulation means only one thing: A machine was there before (Amiga) and another machine (PC?) which is different by design(!) tries to do the same things in the same way as the emulated machine.
Java is not emulation. There is no original bytecode machine. An FPGA-Amiga emulates the original 68000 CPU but not the Amiga (which is more than the sum of its part), because it is really a machine that works the same way the original does.
Natively on the other hand just means that you can run it out of the box without adding anything (like a ROM file).
Oh, and WINE is not an emulator, only because it doesn't try to run Windows programs the same way the PC with windows would. It runs them the way linux would. Else it would be an emulator! AROS is similar in a way.
