“Even if Vaad of 5 towns or Vaad of Elizabeth visits DD randomly throughout the day, if there’s no shomer shabbos there, how do you know they’re not using the microwave for their own food when the rabbi isn’t visiting once or twice a day?”
I think the logic is that since a Mashgiach can walk in at any moment, and they know that if they are caught doing that when the Mashgiach walks in, we can assume everything is ok. If you don’t use logic like this then there would even be a problem with a Mashgiach Temidi. What’s stopping a worker from secretly putting treif in the food?