Welcome to the club. It happened to me. I planned to check the axle fluid early on, and before I knew it, I had about 20 hours on the tractor. (I had checked everything else.) I finally checked it, and just my luck, no oil in the upper part of the axle assembly. I think I added around 3 quarts, like you. So, mine had about 1 1/2 qts plus or minus in it.
Kubota really needs to have some type of plastic flag on the fill plug saying something like, "Fill before use", which can be removed after filling. Yes, it should not be necessary, but there are too many stupid/lazy/incompetent people out there. It is really inexcusable for any dealer to have this happen, and it happens often. It was also inexcusable for me to trust that it would be filled when I received it.