The dealer comment "let it wear in" indicates questionable knowledge of the Kubota gearbox. The component parts -gears, bearings, splined shafts, shifter forks etc.- are designed and manufactured to close tolerances. The gears are finished beautifully so the "wear in" is essentially zero. If something is out of tolerance or mis-assembled enough to make noise, it should be inspected BEFORE it causes more damage.
In the old crude days (and on some recent Zetors) the first oil change of a large tractor tranny brought out half a cup of filings and metal debris. The gears and other parts were so big they survived a long time anyway. But a Kubota gearbox is a classy piece of work and should not make extra noise on changing torque direction.
If your dealer will not take this seriously, insist on involving Kubota's service rep. If it is abnormal Kubota will likely fix it if they know about it. My 2 cents.