Either one will work and there is no difference. Kubota does this because most of their engines are used in other aplications where one oil fill may be completly blocked. I am pretty shure I used the valve cover hole to fill my b2650.
Same for JD and Isuzu. One on top will take higher flow without backing out because it's straight in and not at a slant. Just stick a funnel in it and pour. Cannot do this with the side one.