I can see the motivation for a seating chart in a cafeteria. Not that I necessarily think it's a good idea -- I think it's a band-aid sort of solution that needs to be addressed at a different level, particularly in a Christian school.

Cafeterias can become places where cliques reign and a lot of social abuse can take place. For most of junior high and to a lesser extent in high school, I was the kid who, when I came to sit down at one part of the table, other people would go into a highly dramatic and histrionic performance of trying to get as far from me as possible, or telling me to go somewhere else or I'd get hit (depending on whether it was the "cool kids" or the rough kids in question. My hygiene was fine, FWIW. I just had been marked out as the Person in the School Who Will Be Treated That Way, I suppose because of awkwardness.) Enforced seating eliminates this kind of thing. It doesn't make the cruel kids good, but it spares the pariahs a certain amount of humiliation and allows them to eat their lunches more or less in peace. It also cuts down on making lunch time the time for the cultivation of cliquishness and other undesirable behavior, by not allowing the kids to set up their own class-based seating arrangements.

There are better ways to do this, such as teaching the kids to treat one another with Christian grace through genuine discipleship, and enforcing a minimal standard of external decency where that doesn't take root, but like I said, I can see the motivation, at least.

Anyhow, poor Anne. Just remind him that tucking his shirt in couldn't possibly be more unpleasant than serving detention and writing pointless lines, and if he chooses to stew in detention, that it is entirely and completely his own fault. Beyond that, grin, bear it, and pray!