I have my suspicions that AbM was told by his dad what happened, but doesn't want to have to be the one who exposes his father to the justice system. That's why he's so upset and begging his dad just to tell the truth. Just an opinion based upon his behavior, though. I admit there are holes in the theory, since he is willing to expose him to the public on a television show.
After watching the Disappeared epi, I agree. He seems to be feeling a lot of anxiety and guilt. Suspicious polygraph results can occur when people are hiding information about a crime they didn't commit, usually to protect someone else. The dad may not have directly told him that he killed his mother, but AbM possibly saw or heard more than he revealed.
The family has been raised by a controlling, authoritarian sociopath. To an extent, the sons were financially dependent on him and probably feel a tremendous amount of guilt for not doing more to protect their mother or get her the help she desperately needed. When Linn's sister mentioned her having a black eye from falling at home, IMO, that raised a red flag for domestic violence. The sons and their families likely saw a lot of violence against their mother growing up and were likely victims themselves.
Trying to figure out what the father was up to when he had the meltdown over the 4 wheeler. Was he angry because he wanted it to hide Linn's body? Did he use the truck instead? Or did AbM give him the 4 wheeler that night and in some way assist in helping his dad to hide her body?
Kudos for local LE turning so much of the investigation (including evidence) over to the FBI and ME in St. Louis. Given the nature of the dad's activities, they're probably under a lot of social pressure to sweep it under the rug.
JMO