I think I know why it is there, as an engineer in embedded electronics. I think reverse voltage fed by free-spinning fan was inducing noise on ground wires (-) that they suspected was frying their voltage regulator which was then overcharging batteries which had then troubles delivering voltage under load leading to starting problems and even unreliable ignition. While the source of the problem is narrow hysteresis and the number of on/off cycles for the fan when it works, having as much as 30% of its life spent as free-spinning flywheel generator.
The other problem is, if the mechanic pointed at this part as a reason of unreliable idle and fuel flow at high temp, I am starting to doubt about his skills as he misunderstood KYC-D421 for something related to ignition.
What I did not understand, why entire family of KYC-D421 has so many versions and even incompatible plugs and wiring without additional information. Additionally I have no confirmation if KYC-D421 I see in my motorcycle is indeed EMI FILTER FAN MOTOR 39100-KHD8-9000 - on the partlist manual it loooks.. different.