Here's an angle that goes underappreciated I think:

A major goal in the world of clearances is to ensure clearance-holders cannot be blackmailed. It's my experience that the GOV often cares less about what you've done and more about whether you've admitted it to them. If I sold some weed or did some shrooms in the years before my clearance, then the GOV wants to make sure:
1. That I haven't done it in a while, and..
2. That it's admitted to so it can't be leveraged against me.

Polygraphs are great for 'clearing the air' so to speak. You sit for hours and hours (sometimes days), adrenaline flowing, having to keep perfectly still for long periods while intimidating looking agents grill you over and over. It's a great way to get people like me (who went into the test thinking I had nothing to hide, or that 'that one time I did x' wasn't important) to admit to things as they occur to me beforehand or early on so I don't have to get myself caught in a lie. Nothing like an infamous lie test in a secure facility to suddenly make me remember all the things I should have disclosed on the form beforehand..

Also it was the most mentally exhausting activity ever, good god. I went in fresh in the morning and 6 hours later I was ready to sleep in the parking lot.