I had the same thought. I think the hardest part could be "diffing" the outputs, though. Is some particular difference within expected parameters, or can you really detect that hidden bit of metal on layer 5 of the board? Interestingly I stumbled upon this: http://www.sandia.gov/mstc/fabrication/index.html

That's not going to happen because the two toolchains won't be anything alike. You won't be able to make them alike either. Worse, that people often quote Thompson's attack shows that INFOSEC teaches subversion very poorly: it's the least likely attack to affect you and you really need to counter the others. What you have to do is make the software correct, make it secure, and ensure no subversion in lifecycle. That's called high assurance or robustness system design. Links below show you how to do that.

High assurance software design - nice intro http://web.cecs.pdx.edu/~hook/cs491sp08/AssuranceSp08.ppt

FOSS tools for high assurance http://www.dwheeler.com/essays/high-assurance-floss.html

Certified compilation (HW w/ need certified "synthesis") http://compcert.inria.fr/

Original work on subversion http://csrc.nist.gov/publications/history/myer80.pdf

Example of it in action http://www.cisr.us/downloads/theses/02thesis_anderson.pdf

Example of high assurance hardware (AAMP7G version is secure but no public paper...) http://www.csl.sri.com/papers/wift95/wift95.pdf