Drain holes let water out, but also allow moisture in the form of water vapor in, and with variations in temperature, "breathing" occurs. In practice, assuming the drain hole is properly located, studies show that only a minimal amount of internal corrosion will occur. But also that with a properly welded, sealed structure, no detectable amount of internal corrosion occurs. For corrosion to occur, besides the reactive metal, there needs to be water or water vapor and oxygen - - in a sealed structure, once either have been used up in the oxidation process, no further corrosion occurs.
There's may be several things going on here, and all look to be Kubota's fault, poor material quality or welding, and/or stress corrosion cracking.
I wouldn't be drilling additional drain holes on my Kubota. If properly designed and built without them, they should not be needed. If one does add them, I'd think there would would be no recourse with the manufacturer and little likelihood of them stepping in to cover the modified product.
bumper