Keep NOPs when comparing with original binary (#2931)

We have a check that ensures that the optimizer did not change the
binary when it says that it did not.  However, when the binary is
converted back to a binary, we made a decision to remove OpNop
instructions.  This means that any spv file that contains a NOP
originally will fail this check.

To get around this, we convert the module to a second binary that keeps
the OpNop instructions.  That binary is compared against the original.

Fixes https://crbug.com/1010191