Why is this circuit using a branched 5V wire?
It is drawn as a conceptual wiring diagram how to do it, like how a schematic represents a device. How to actually realize the conceptual wiring in physical world with physical components is another thing, like how the actual PCB for a device is drawn from the schematics.
Since you don't have T shaped wires, you can do it like you suggest in the second picture and use the protoboard as a junction.