I’m making an educated guess as I’m not familiar with that Kubota model.
Engines often are used in a variety of machines/applications. What might be in a tractor or excavator could also be used in a generator set, refrigeration unit or marine application.
They sometimes have “extra” oil fill ports on them to accommodate the different applications/configurations that they may be used. Those ports likely lead to the same sump/oil pan, but aren’t as accessible in different configurations.
If you research the model of the engine itself, you may find reference to the additional fill ports.