Perhaps it's not changing those VCDS settings, but sending it's own signals
Illustrative guess:
Normal: User presses indicator stalk down a bit > gateway receives this command > gateway checks in comfort indicators are on > gateway checks number of flashes setting (vcds setting) > gateway makes indicator flash x times
PolarFIS+: User presses indicator stalk down > PolarFIS+ receives this command > checks it's own stored setting value > sends command to gateway to flash indicator light x times (as if you fully pushed the stalk down and then flicked it back up after x flashes).
Same with mirror lowering, perhaps it just sends the same electric signal to the gateway that would normally get sent when you push the mirror switch (sort of like recording a Macro in MS Excel)