These are my thoughts on some of the many things that are unclear. This all assumes POI alone is guilty, and his family is innocent, having believed his story. MOO
I don't think the "wife" referenced in the 911 call is POI's. It's MOO that POI is single. The aunt making the call was EXTREMELY rattled, and is trying to repeat what JM's parents have told her in a very jumbled way, while trying to keep the family calm. I do suspect that "him" and "his wife" are whoever lives at the farm, probably POI's parents the owners.
It is clear now that JM was working on a farm in Washington Township (video evidence showing an LE vehicle leaving "the farm where JM worked"), even though all MSM reported it to be near New Harrisburg earlier. The farm belongs to POI's father so it's likely his parents live on the farmyard.
I believe that JM was indeed at the farm (alive) through the Sat. morning milking. We don't know if anyone else was actually in the barn and saw JM there, but it sounds like the milking schedule was set up to have at least two people working at a time. So, if something had happened to JM while at the POI's house overnight, the POI would have had to ask someone else to help him in order to get done on schedule. Then he would have told a different story, or timeline at least.
I think that POI and JM did return to the POI's house in New Harrisburg at noon Sat. Or if the media was wrong, I've wondered if he lived just southwest of there near the Baxter Ridge church area where LE focused searching.
I lived with a dairy family once, and they never got enough sleep between milkings and took naps every chance they got. So, MOO, I think after eating some lunch, POI took - and shared with JM - drugs of some kind prior to a nap.
Then, the scenario I'm leaning towards right now is that either JM died soon after taking the drug; or, when POI woke up to leave for the dairy, he discovered JM dead. So if he's had several drug incidents already, he knows he's in HUGE trouble no matter how accidental the death was. He also knows he's got to start the milking on time (or the cows will let everyone in the county know by loudly mooing), so he takes the body with him to the farm, quickly buries it and heads to the barn.
But now he needs help with the milking (and an alibis) so he tells someone (his dad or mom if they live there?) the "JM stayed back at my house with a toothache so his mom could come get him" story, and asks for someone else to help him.
Then at 7:30 the milking is done, and POI, probably in the presence of someone at the farm, called JM's parents to "make sure JM had gotten home." Of course, they go ballistic, thinking they missed his calls and he's been at the POIs house alone for 4+ hours. This is where I think "the wife," (POI's mom or whoever lives there,) "took off" to check POI's house. But that may not have happened at all ... But somebody will have gone to POI's house, JM isn't there, and family thinks maybe JM panicked at not being able to get ahold of anyone and tried to walk home.
My last thought is about why there may not be an arrest yet. Even if drugs were not involved in JM's death, is it possible that when LE searched POI's house they found drug paraphernalia, and feeling suspicious about the whole situation they arrested POI on "charges unrelated to the dissappearance"? Maybe he's actually in jail so they can safely take their time to "get it right".