I am just flabbergasted that anyone would think that a 12-year-old would pee on the carpet for no reason other than "laziness". That's incredibly naive and simplistic. You've got a lot to learn about human nature, and I feel sorry for your child if you don't figure it out pretty soon.
To the OP, I am glad to hear the update. It's a testament to your relationship with your son that he felt safe opening up to you about something that no doubt feels shameful to him.
About being afraid of the dark -- up until I was an adult every time I climbed the stairs from my parents basement I had the creepy feeling that something was behind me. I knew it was irrational, but I couldn't stop myself from feeling that way. (It was based in a childhood incident, I believe.) I saw weird things in the dark too, and had night terrors until I was an adult. Developmentally, some things take longer than others for us to grow out of. Irrational fears aren't only the stuff of childhood. And after all, your son isn't exactly an adult yet, right?
to you and son.