Something doesn't seem quite right about this story. He made a clock and then chose to store it in a metal briefcase with the numbers on the outside. In other words, he built something that looks exactly like a bomb from a movie: briefcase with red numbers on it. Maybe this appearance was entirely accidental; but I would bet that he originally intended it to look like a bomb, probably for humour.
And it started beeping in class- depending on the kid's history/attitude sending them to an administrator is not an over-reaction. The zero-tolerance b.s. that happens next is the problem, but even there it's hard to blame administration- I'm sure there's zero tolerance for anything that looks like a weapon, and unfortunately a beeping case full of electronics qualifies.