To me, these are the only scenarios that make sense:
1. It is a planned parental kidnapping/abduction by or/and orchestrated by Seth. Motive: revenge, hate on the Proudfoots, "want's to show them
how bad parents they really are". He planned with Sebastian on Thursday when they were going to meet up and how (just outside cameras and just outside the house). (Seth as LE experience). This means he must have psychopathic tendencies to be able to torture the mother of his son to this degree. Does he? If Seth's alibi checks: He needs an accomplish to do this. Either something goes wrong here (Fargo-style) or Seth is a true and convincing psychopath (I am not saying he is, this is JUST a theory).
2. Sebastian unalived. The "thud" was it. Kate found him, perhaps hours later. She was convinced by Chris to "cover up". He doesn't want to loose the custody battle with his daughter, he threatens to leave Kate and tells her "he is already dead". They plan it all. Chris drives there at night, the body is dumped on the way back to Memphis. They lie.
I don't see how Kate can lie so well, as a mother to that boy. and over time. It seems quite unlikley. But, if she is truly in denial and traumatized by the event and what followed - it is a possibility.
3. Sebastian did know someone that none of the parents knew. A person he trusted. Outside all the family drama. In regard to, how all guardians in his life have acted, he was in need of a person who "saw him" and he could be a perfect victim for a predator. BUT - this predator needs to be close: meaning: a teacher, a neighbor, therapist - someone he communicated with offline.
If he was punished by Kate that night, left outside without shoes: he was sick of it. He left and he ran into that person. If that is true: he is not alive. And they have a serial predator in the area... Which means there much be evidence already (some kind) of an "odd character".
Challenge me!