Big caveat there. Sony later removed the ability to install "OtherOS" (a.k.a. Linux or FreeBSD) on PS3s from those models. [0] I wonder if that firmware update basically neutered the supercomputer or if they were able to keep them from updating automatically.
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.
Seems to me like that'd be more reason to offer a support contract and recoup some of the profits lost from the lack of game sales.
https://www.syracuse.com/news/2011/03/rome_labs_supercompute...
> Rome Lab asked the Department of Defense for $2.5 million to assemble its supercomputer. By the time money to buy that many was approved in 2009, PlayStation 3s were hard to find. Rome Lab bought as many as they could — 1,700.