Okay, not a runaway.
Maybe an accident. Dylan is to young to drive and no vehicle is missing so I'm ruling out car accident, unless Dad has a missing vehicle he isn't reporting. Not likely, MOO.
Fatal skiing accident, run over by a vehicle, wild animal attack, etc., there would be some kind of remains or vast amounts of blood, someone would have seen signs by now or found a body.
Foul play. Strangers do their thing and ditch the evidence. They don't hang around cleaning up crime scenes and pondering where to hide the body, they just dump it and run. Time is the enemy and distance is their friend. If some freak was lucky enough to get this boy out of the house and in to a vehicle with all of his belongings in his backpack and no evidence of a struggle, where would he go from there? Some private place near by? Not likely. Walls are thin in cheap motels, lots of people. I think that a stranger perv would hi-tail it across one of the nearby state borders. Do the murder in one state, ditch the body in another. There are three other states within a couple hours drive. Makes it harder to investigate, increases potential for in-fighting between jurisdictions, increases opportunity to slither right past LE while they are figuring out who is in charge.
Foul play in the home. Just a possibility. Whether it was pre-meditated or an un-intended result of anger or carelessness, it is a crime to conceal a death. If a loved one ends up dead someone has to either make a proper report with police or find a way to conceal it. Obviously there was no report of a death, accidental or otherwise. Dylan was reported as being missing. Dad wants him to "come back" home. He is not looking for a kidnapper, he is asking Dylan to come home, as if he had left on his own and could return if he chose to. Police don't seem to agree.
When a person is killed by someone close to them, that person generally has a bit more time make a plan. No one will suspect a problem until they raise the alarm. They have time to clean up, get rid of ...things. Make up a plausible story, distance their own involvement with a staged alibi. How many times have we heard, "I came home and he/she was just gone/dead."?
No phone activity after 8pm from a p'd off 13 year old boy. Eager to meet up with his old buddies. Not likely he was having so much fun with Dad that he just decided to turn that phone all of the way off...not use the silence feature. Kids use their phones to tell time, listen to music and check the weather if they are planning outdoor sports such as fishing or skiing or dirt biking. They use the alarm to wake up if they have plans. If he didn't want it to ring, "silent" is a flick of a button.