Think of it this way, the board only has a header that can support 2 USB 3.0 ports. If you use the supplied box, that occupies those 2 ports. If you don't, then the port built into the case has somewhere to go.
You alternatively could get a USB3.0 PCI card that has internal ports (not the most common but they exist). This would let you have the box as well as somewhere to connect the case's port..