I think the point is that the answers on the polygraph didn't indicate his guilt in the 3MW case.
However, his low IQ and personality disorders impact polygraphs in similar ways as psychopathy. I don't think any polygraph would be reliable. One of the problems with Hall as a serial killer is that he lies and denies and then admits what he just denied. And so on. The Springfield PD claims to have investigated Hall's confession (made to his brother and to several writers) that he killed the 3MW. He was known to be active in the Springfield area at different times. He stalked victims at convenience stores and other venues, often picking them up when the opportunity presented itself. He used a van as a killing/abduction site. He threw victims in rivers and dumped them in fields and in the Mark Twain Forest. He used various ways to kill females and their ages ranged from 10 to the late 50s. He claims to have operated alone, with one partner, and with 2. He did home invasions. He worked as a janitor and according to one source cleaned his van to the point where there were only 5 fingerprints--all his. (I'm summarizing a lot of stuff I read on the web here, most from a book Urges: A Chronicle of Serial Killer Larry Hall.)
Springfield PD is not the only LE department skeptical about Hall, but he's serving life in prison for an abduction (they couldn't get him on murder because the girl's body, dumped in a farm field, was destroyed by a farm combine). All I will say is that I've come to think that someone like Hall (or a group including someone like Hall) was responsible for the abduction. Someone who stalked women, had a killing van, was willing to do home invasions, and felt comfortable with a range of ways to abduct victims.