I felt like the article spent way too many words to explain the idea of "the agency shared data across the air gap using USB drives, and a vulnerability was used to surreptitiously copy the malware onto the USB and then onto the target machine", and AFAICT none on explaining what that vulnerability is or why it exists (or existed). Then the rest is standard malware-reversing stuff that doesn't say anything interesting except to other malware reverse engineers. The inner workings of the tools aren't interesting from a security perspective; the compromise of the air gap is.

(As for acoustic etc. side-channel attacks: these would require a level of physical access at which point the air gap is moot. E.g. if you can get a physical listening device into the room to listen to fan noise etc. and deduce something about the computation currently being performed, and then eventually turn that into espionage... you could far more easily just directly use the listening device for espionage in the form of listening to the humans operating the computers.)