Yours seems like a good question, really, and made me think.

I think it's a matter of context.  To a Java programmer, machine code is not
"really" an intermediate step to microcode - the machine code defines the
native platform from Java's point of view (and the JVM's).  But in real
reality, we demigods know the JVM is mistaken.

For the sake of discussion, it is useful to forget microcode exists when in
Javaworld.

When I said,

I was referring to the difference in machine code, not microcode, between a
pre-compiled executable, which is what the OP had discussed, and that same
executable when it's actually executing, same as Mike.  All those relocatable
addresses get real selectors, object modules get linked, DLLs get called, and
only then as the program executes do you get a reasonable facsimile of "native
format".  No reference to microcode is necessary to make this point, although
in fact it strengthens the point I was making.

Even in machine-language terms, the CPU does a sort of JIT by re-ordering
instructions, caching results, manipulating registers, prefetching operands
and a host of interpretive acts.  The discussion had fallen into the trap of
thinking that statically pre-compiled object modules in machine language would
handle all that better than a bytecode-compiled class running in the JVM.

They had missed the point that, even in machine-language terms, that
"compiled" executable is far from ready to run, nor does it specify precisely
or even predictably exactly how those machine instructions will execute.  The
JVM, by virtue of its ability to adapt to runtime considerations and to
globally balance actual usage patterns, often "recompiles" or reorganizes the
instructions into a more efficient pattern than the OS can when it
"recompiles" the machine-code executable.

My argument is that precompiled machine-language executables are an
intermediate format to a runtime machine-language executable, even without
regard to microcode.