It seems like if you can have the tools alter the embedded timestamp (even as a post-processing step), you can match the binaries pretty closely. The last bit

It seems like if you can have the tools alter the embedded timestamp (even as a post-processing step), you can match the binaries pretty closely. The last bit is the signature, which you can't duplicate, but you can also just take out, as it's not code. But, if you're paranoid about that, zero-out or remove the signature after verifying it.