This article is trying to show it as more scary than it is. The key points are: this is systems up to secret level only and sessions are recorded and watched by an escort; the escort is not as tech savvy as the engineers performing maintenance (who are also Microsoft employees, from many countries of origin) but there are other controls too; they can’t just run unsigned code etc. The top secret stuff isn’t using this…
Along with everyone else they interviewed apparently, I had no idea this program even existed, but there have always been similar programs for other kinds of maintenance and support personnel. The people who repair the toilets and refrigerators in a SCIF don't have clearances. They get an escort, and everyone else in the building gets a warning before anyone needing an escort comes in, telling them to put away any sensitive data and either work on something unclassified or turn off your monitors and stop working completely until these people are done and leave again.