My compromise theory, based on the publicly available evidence and Occam's Razor, is this:

1) Boy takes a commercial clock out of its case, and puts it into a pencil case to show to his friends — either because he just thought it looks cool, or because he thought it looked like a bomb and he wanted to prank his friends. (Boys will be boys.)

2) School and police overreact, as they have many times in recent years (in different cases involving children of different races/religions) as a result of terrible "Zero Tolerance" policies.

3) Boy's father, Islamic(Islamist?) cleric, political advocate, and participant in past publicity stunts, now (after the fact) sees it as an opportunity to advance his "portraying America as islamophobic" agenda, and goes 'all in' with the media publicity, resulting in high-profile and pretty clearly staged/coached press and social media appearances for the boy.