What you are referring to are embedded assets. Embedded assets are different than trained spies in intel or counter intel. A trained spy may be a handler of assets but they generally do intel work themselves and usually have some form of cover. A trained agency spy will undoubtedly be able to beat a poly and are trained to do so, on a regular basis. While the accuracy of a poly is too low to be usable for the discerning of truth, they do work to some degree. They are better at telling what you said was true than they are at telling what you said was a lie. So generally if a question is asked and you don't pop then it is fairly safe to assume that you told the truth. Where their completely fail, is sometimes they will pop when you are telling the truth and you can train yourself to not set off the machine when you lie. The problem is it works on the right kind of person in a clean room setting, but that is never the real world, there are just too many variables that are not handled for it to be anything other than a psychops tool, where it just becomes a loose guide on where to dig deeper.

Fun fact, lie detectors are completely ineffective on compulsive liars.

I'll say it again: they don't work.

You can't really use them for anything. A polygraph machine might have an application though: doorstop.