Nothing wrong with this.
The problem is that if you ever drop something onto the mobo, you could be in trouble.
Also, if you have kids/pets, then you will also eventually run into problems.
I don't think this would be a fire hazard. To catch on fire, you would need sustained sparking (arcing) and even then I doubt the box would catch on fire. As an experiment, try putting a lit match on top of the box and I would bet that the match would burn out before the mobo box catches fire.