Earlier quoted context omitted.
Sitting still is not a virtue. It literally accomplishes nothing. It's a secondary detail - whether or not the kid is sitting still does not tell you whether they're actually paying attention to the lecture and whether they're going to remember it.
You're taking a narrow perspective. Fidgeting is distracting, to everyone else. Whatever your ideals of a perfect world may be, 20 dump trucks of kids needs to be educated at one facility every day. Whatever you may think one kid is doing to help him focus, that kid is disrupting the focus of his 8 neighbors. Something needs to change, but it's more than just perspectives.
Whatever else Catholic churches may get wrong, apparently all of the "modern" ones I've ever been inside figured out the "crying room" technology a long time ago. Setting up a "sound diode" isn't all that difficult with modern technology. If whats really important is forcing future factory workers to line up in alphabetical order in row/column format, then flexibility might not work.