We know that Amazon had Intel create custom chips specially for them, like the E5-2666 v3. So of course Uncle Sam have their own top secret bespoke Intel SKUs.
Amazon buys a significant fraction of the chips produced by Intel. I don't know how many security-sensitive chips the US government needs, but I'd be willing to bet it's a drop in the ocean.
Mostly the same chips everybody else does, but made in a special purpose fab in the US. This extends to everything in a computer (even firmware etc.). This means that a computer for use in classified settings is a LOT more expensive than your average desktop.
