As the Not the Bee author points out the box and nails were designed by an intelligence, and it was an intelligence that shook the box that brought those nails into alignment.
In physics there is the Anthropic Principle. This is applicable here. The Anthropic Principle states that the universe is fine-tuned to our existence; change any one physical law, no matter how small, and life becomes impossible. We exist ONLY in this universe, which seems tailor made for us.
There are other variants on the Anthropic Principle. The "Weak" Anthropic Principle admits this is so but argues that we are just seeing what we want to see, or what is in front of us. We evolved into THIS reality so naturally we assume no life is possible in another.
But even if that is true it still doesn't change the facts; our existence here was a miracle, something that should not have happened.
In fact most atheist scientists subscribe to the Many Worlds Hypothesis, which says there are an INFINITE number of universes, each with slightly varying physical laws, and that random chance guaranteed that life would arise in at least one of them. It's the only way to get around the philosophical implications of the Anthroopic Principle. (Many worlds is not the Multiverse, btw; the Multiverse suggests there are different universes sitting next to each-other in a larger megaverse and not interacting because they are too distant from each other and have slightly different physical laws. Many Worlds is based on quantum physics and the Copenhagen Interpretation which says that a new universe is generated at every decision point since two or more contradictory events actually happen at once and thus create a new universe, like cutting slices of bread from the loaves Jesus multiplied at the Sermon on the Mount.)
At any rate the Anthropic Principle has long been the bane of atheists and for good reason.
Anyway, I would suggest this guy choose nails of different weights and sizes and see if that works. Or even better, put some different sized bolts and nuts together in there and see if he can shake them into attaching themselves, which is basically what the atheist crowd argues happened with abiogenesis in the first place.
This little nail-in-box experiment does not prove order comes from chaos but that something purposely designed to be orderly will return to a state of order if enough energy is applied in the proper way. But we've always known that; it's what happens when you design something to be so.