Deconstructing the crate means that only construction bots can empty the contents of the crate. I don't have lots of construction bots on my logistic driven mining facilities. I'd rather deconstruct these myself.

You've probably found it by now, but there is a setting under Map that allows you to disable chest deconstruction.

There are now two more solutions to this: The mod will wait until the chest is empty or scheduled bot pickups are complete. Or you can add the names of the logistics chest to the blacklist setting.