When you are on the box, the toros is much closer to vertical, which causes a decrease in the shearing force on the spine, and an increase in compressive force. The spine is able to bear a much greater degree of compressive force than it ever could shearing force, which can damage the discs.
Anyone who says that box squatting is dangerous because of the pause has no idea what they are talking about, as they are only considering a single factor of a complex equation. And exercises for spinal unloading, such as reverse hypers, help open the spinal column, specifically the lubar vertebrae, and increase the flow of synovial fluid.