I just took the Poly for a 3 letter agency. It really sucked especially since I already work for another agency and was trying to jump ship. Anyway I know some of the workings of federal employees and federal contractors like polygraph operators.

All federal agencies are sensitive to complaints. Of course one or two complaints are par for the course but they also believe in the saying of "where there is smoke there is fire" philosophy. 

So if you are an applicant and undergo the polygraph exam, at the end of the interview before you leave, the examiner will tell you if you passed or failed. Then he will ask you a series of questions about your experience such as:
1. Did you think this interview was conducted professionally?
2. Would you choose me again to conduct a polygraph.
and so on. Those are CYA questions that cover him from complaints because when you leave and reflect on the experience, you are going to realize the extent of the abuse he put you through and become angry. That will anger will become even more so when you get the you failed and your application is terminated letter. Unfortunately you already gave him a glowing review before you left in the hopes that being nice will save you.

Don't. give him a good review. 

After the polygraph process, when he tells you that you failed and he tries to tell you that it isnt his decision but the next level after him, he is lying. When he said you failed, you failed. So when he asks the post interview questions, don't be a nice guy because it will not work.

Dont get mad and tell him what a farce this whole experience was. You need to very calmly state how unprofessional his conduct was. Remember every time he raised his voice, got angry, called you a liar, etc and bring that up during the post interview. It won't save you but at least he will have to answer to his supervisor why his conduct was unprofessional. We all know his behavior is part of the act, but no one ever calls them out on it. Be that person that does.