I'd be willing to believe in factory overclocks, one magic speed bin that wasn't common enough to market to the public, but was common enough to yield a few here or there. I worked at a place that was able to secure factory overclocks from Intel, 100MHz faster than what everyone else was buying.
Factory overclock, and in those days Motorola could probably have given them a batch of mid-development DSP chips (sort of proto 56002) that could clock much higher and still sit on the unmodified motherboard, max out the scratchpad memory, etc. Then the add-on cards. Anything that was potentially involved in nuclear response decisions probably could get a lot of budget. It would be interesting to inspect the hardware that still exists to see if there are any signs of what exactly actually happened.