kubota never tells anyone why they change a part number. On ECU's I'm surprised it hasn't been changed much more often, a lot of mfg's do that. Vendor changes, color changes, and the many software changes on pre-programmed ecu's. Gotta keep the epa happy.
Then they have enhancements. If kubota sees a high failure rate of zener diodes within the ecu, they'll ask bosch (or whomever the maker of the ecu is) to beef that area up, which can entail other changes, negating a new part number.
or if the ecu stands out like a sore thumb and kubota says paint it gray, yes another part number. Or if the gray paint doesn't quite match the frame. Another part number. OR (here's a good one) if the fenders coloring fade to pink, they'll change the paint process and yes another part number. I think some of the older M series guys can relate to the pink kubota statement....
or if the original vendor (who supplies it to kubota) jacks the cost up 250% and kubota can find another one from a different vendor, with the same program, connection, etc, for 5% more than what it was, they'll change the vendors--and thus the part number.
assigning a part number to an original part doesn't mean that part is going to remain the same throughout it's service life. FORD...FORD's internal part numbering system, if one doesn't know a little about it, will confuse the daylights out of you. They're notorious for this. So is Yamaha. All manufacturers do it, be it to save cost, to improve the product, meet standards, whatever-but they often change the part many times in it's lifetime.
The end result is that consumers (myself included) look at it all as purposeful deliberate confusion.