1. No one updates supercomputers automatically. Instead you firewall the compute nodes and have a team dedicated to maintenance and support to do periodic upgrades.

2. I'm sure they had a support contract, which may have included running an entirely different firmware. I have no specific knowledge, but based on other supercomputers I've worked with, these are often very custom machines, despite the "commodity" hardware. The odds that they were running the consumer version of the firmware are low to nil.