I agree that VM's byte codes are very different from real machine code. My point was to just remind everyone of a KNOWN similar thing that has been addressed by the crackers.
About changing the meaning of byte code or as you say, changing the instruction table to another one, we are not in fact changing anything but may add one (easy) level of protection to the scheme.
But all in all, I agree that using emulation can make cracking much more difficult and personally, being an old guy that I am, would not be really interested to crack such a traget unless there is a big motivation for that