I have a sneaking suspicion that the counterintelligence right hand doesn't know what the left hand is doing.  They know they like polygraphs (both because of appearances and likely because at least some of the decisionmakers believe they work).  They know that they have more applicants than positions, and a limited budget.  So I think someone said "get rid of some of the applicants as cheaply as possible", and someone else translated this into "let's use the polygraph to thin the population".  

Skeptic