Just jumping off a part of your post.
What if Dylan left Sunday, after MR went to bed. (There wouldn't even have to be an argument, just a kid wanting to see his friends without thinking things through.)
MR gets up the next morning thinking Dylan went up to bed. Maybe he knocks or calls out for him to get up and in getting no response goes into town thinking he'll let him sleep. When MR gets home, he thinks Dylan is still sleeping and goes to wake him, finding that Dylan has not be in his room/bed at all. Realizing how bad it will sound that he didn't even know he had left and the legal problems that will follow he searches on his own, figuring Dylan is probably at R's house. This might explain the changing stories of that morning.
Also this would explain why no one saw Dylan leave Monday morning.
Dylan could have been picked up by anyone that night or hit by a car, a lot of deer run into the road in CO, someone may not have even realized it was not an animal. (Hate writing that last sentence)
Does this make any sense?
/MOO