Your story reminds me a little of Ed Snowden's description of his experiences working in secure environments in Permanent Record.
Each individual measure may make sense in isolation, but just like with any long-lived project, the sum total of all of them can absolutely still add up to absurdity.
Many years ago I worked as a contractor at a financial institution that was a little full of themselves. I had to be escorted from the entrance, through the main office, to a smaller, "less secure" room inside the main office. The bathrooms were a short walk away from the less secure room through the main office so I had to have an escort to go to the bathroom. The escort would wait outside the bathroom for me and escort me back to my desk. While annoying and inconvenient (and ridiculous) it wasn't really a big deal until I came out of the bathroom one day to find the escort had disappeared. (I later found out he had someone kind of family emergency and had to run home, I guess dire enough that he didn't have time to inform me.) I asked around the office where my escort had gone but no one knew so I walked back to my desk on my own.
The next day the CTO called me into his office and said he should have me fired right then and there for violating security protocols. I explained what had happened but he didn't care because it looked bad for him. Apparently I should have had someone call security to escort me back to my desk.
Two months later they started construction on the room I was in to provide a path to an exit that didn't go through the main office. To use the bathroom I had to go through that exit and leave the building, walk outside to the main entrance and use the "non-secure" bathroom and then be escorted back to my desk through the office.
if you spend enough working in, around or near a SCIF it becomes pretty mundane.
the windowless rooms and sterile environment are actually not much different from commercial telecom stuff, like if you meet a person who works for an ILEC and has a desk in a CO.
stick your cellphone in the little shelf box outside the entrance to the secured area, pick it up when you leave, etc.
I found telecom environments to be similarly sterile but more competently designed and managed than SCIFs.
Maybe this is unfair and what seem to be failures are actually by design. Maybe the soul crushing environment is a necessary condition to be in the right frame of mind to inhibit ethical analysis and implement DoD policy.
I worked on DoD projects that I later realized were unethical, or at least unethically used. Yes, I do think that my current work is less likely to be used for terrible purposes just to get someone promoted.
Each individual measure may make sense in isolation, but just like with any long-lived project, the sum total of all of them can absolutely still add up to absurdity.