You must recognize that the wiring diagrams are not exact representations of where wires actually are both on the tractor and within the harness. They are a schematic representation (aka a sketch) to help explain and demonstrate what connects to what.
The connecting of the two wires is shown taking place at the opposite end of the main battery cable to what the owner sees but, from a design and maintenance point of view those two circuits are connected and further nothing gets into the tractor electrical system without passing through the fusible link save and except the current between the battery and starter.
When you move to more involved wiring say in an industrial setting, you will have both a ladder wiring diagram and a schematic diagram.
Neither is intended for production of the harness but rather for "in the field," maintenance and troubleshooting.
The wiring diagram Kubota production engineers would hand to the production floor would look nothing like what is in the WSM.
View attachment 45669
This is another wiring diagram from the same manual. It looks different but in reality the wire interconnections are the same.
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Dave