These systems are on 'known good networks' staffed by people who have some of the most extensive vetting you can get.
These are the folks who invented (or funded the development of) RBAC and the like. SELinux came out of NSA, for example. The tech exists, but it's a hastle to work with. If you've got fully-cleared, all-known-good actors, why bother?
It's not like it's on the internet, or accessible in some fashion.
They put a lot of effort into screening staff, but they're also the most attractive target for well-funded adversaries (Russia, China, etc.).
The only stuff I've ever seen come out of NSA and actually used by anyone in government that hasn't been crap has been hardware. SELinux, etc. are a sideshow. Their OS protections as deployed elsewhere in government are primarily COTS or were developed by external contractors (HBSS, etc.), and are actually shittier in a lot of ways than best commercial practice.
1) NSA actually is fairly competent overall, and feigns incompetence as a way to let people bypass legal controls when "useful".
2) NSA is actually incompetent overall, and people like tptacek who say they're wildly beyond the open world are wrong. They obviously have a huge budget and legal protection (legal or illegal) to do whatever they want, but a lot of what someone would want to do is something even I could pull off given the NSA's level of resources.
3) NSA has really fucked up priorities, and for some reason (limited resources, cynical political calculations, expediency, etc.) put all of their effort into offense and none into defense, not even from their #1 threat (insiders). Maybe they also put too much faith in the vetting process and external shell and less on protections within the chewy center. This was pretty common in the commercial world 10-15 years ago (when "use a firewall and AV filters" was the leading security advice). If NSA actually went backward from the 1980s when they strongly believed on internal controls to actually cross over and be inferior to the commercial world, we're kind of screwed.