What is the explanation for the water scene?

I thought they did that to add to the general creepiness, but also to enable

the upside-down water mechanic.

I don't think you could make it through those sections without

being able to last indefinitely underwater without dying.

This is one of the game's hints that

the boy is being mind controlled the entire time. When you mind control others they appear to be able to continue through conditions that would normally kill, like long falls and prolonged periods underwater. Since the boy "survives" drowning, the game is telling us that he is actually being controlled.

I wrote more about the other hints the game gives you for this in my explanation of the game's ending.

If you look closely in the scene, the boy actually drowns. Then, just a bit later, you'll also notice something gets attached to him — when playing through this the first time, I assumed that whatever got attached to him somehow gave him the ability to breathe under water (in fact, I was pressing the action button all the time, and thought I'd saved the boy, ah :P ).

The thing that gets attached to the boy also has a yellow light, much like the mind control helmets you need to put on to solve some puzzles. So I thought that if a yellow-lit helmet can give you mind control powers, why can't a yellow-lit something that gets attached to your chest bring you back to life and give you under water breathing capabilities?