Wow we are the same age basically and I've never been polygraphed in my life and I can't even imagine such going on even for a job around here, especially 40 years ago. And you've had one twice, both job related???
That being said I know a fair bit about them and have looked into them and real polygraphers a fair amount and yes, I think the normal practice is for questions to be submitted and went through with prior. Your pen example is a good one, I came home with a pen I put in my pocket during the work day as I was using it and it also went back with me the next work day in my pocket. Not intentional and I was not stealing. Normally I carry my own, didn't have it that day and out of habit such goes back in the pocket.
Another good example would be sex and cheating. Did you ever cheat on your wife? One person may feel kissing is cheating and the next may not. So then OTHER than kissing have you ever cheated on your wife Alex? Or did you ever discipline your son harshly? Again one may think harsh is a timeout and another may think only spanking means such. As I understand it, these are why questions are gone through first and either adjusted OR not but then with followup exams zeroing in more on the failed questions and discussing the first gives the reason for the false value. Okay OTHER than a time out or taking his phone away, did you ever harshly discipline your son? If they fail again, their explanation they gave isn't going to fly.
That's how I understand them to work and I'd have a hard time believing the govt. sent in some fly by night polygrapher not being more than adequately qualified.
To Bill Clinton: Did you EVER have sex with Monica? And YES BILL oral sex is sex for the purpose of this exam. Imaginary example.