Re: Hmm, If I was working at a secret agency
[...] it greatly benefits certain agencies
Exactly that. Especially given that Intel and AMD are American, and ARM is British, but their chips are used globally. From an agency and gov point of view: What's not to like? I bet they are more upset that this has come to light than they ever were about the existence of those flaws.
I'd also be inclined to wager that there are more flaws like this in CPUs and other chips/hardware. It's no secret after all that the 5 Eyes would like to see backdoors and reversible encryption everywhere.