I know you're talking about a diesel engine, but when I bought my TORO (Before Toro started selling AYP rebadged stuff) Garden Tractor It has a Kawasaki V-twin had a 2 year engine warranty, but if I used Kawasaki oil it was extended to 4 years. I did use the Kawasaki oil only because of the warranty, reasoning I could buy a hell of a lot of oil for the price of a new Kawasaki engine. I only use branded oil, but not the more expensive Kawasaki oil. It is nearly 20 years old and is still not burning any oil.
If one buys Kubota or John Deer brand oil, one doesn't know who refined the oil, so I would imagine that if the specifications are the same, then it should be OK. One can buy a hell of a lot of oil for the price of a Kubota Diesel, so my uninformed suggestion is go with what you feel comfortable with.