Knocking could be a bad injector, or not. Could also be worse, like a spun bearing, though less likely, not saying it couldn't happen. Kubota will figure out what it is and then deal with it as a warranty issue. This is why you, the OP bought a new tractor, right?
IF Kubota says dealer is to do a rebuild on site in their shop, then it's their call. Warranty doesn't give options to the buyer so much as it does the manufacturer and dealer. They're the ones who offer and write the warranty and then stand behind it.
To the OP, sorry your brand new tractor broke with so little hours on it. You did nothing wrong- don't worry, it will get taken care of.
And stages of grief don't go according to a specific sequence- one may experience some or all of the stages at various times, or not. It's OK to be angry about having a broken tractor. And realize it's a machine, and anything assembled by humans or robots can and at times may/will break. Even Kubotas.:confused3: