No, the US government are free to take quotes from anywhere in the world. They DO give preference to many large US firms, though.
The fact is, Apple has a good reputation in the US. Plus, the machine itself is much more available in the US, much more ruggedized (the iServe ships as a rackmount system -- no pain in the arse building), more powerful, and, most likely, one of the people making the decision holds some Apple stock.
Or, alternatively, the only proposal submitted was for the solution they chose. ;-)
But, honestly, it was the right choice for a PPC solution, anyhow. I DO trust the quality and supply of Macs over any Genesi/Eyetech boards, anyway.