Wait a sec. Apart from the fuse, those protective elements are all in parallel with the 5V rail and they would work as intended. The drawing order is irrelevant.
The physical proximity of the TVS diode is relevant for protection purposes. By placing the TVS diode physically close to the USB port, it does a better job at protecting than if you placed it further away. That's because there's impedance of the trace that isn't shown in this circuit diagram that has to be considered for extremely fast transients like what a TVS diode aids with.