Probably because bidirectional controls only work under certain conditions, e.g. engine off, ignition on. I think that error with the engine running means the engine/AC controllers have taken over the fan control.
If the fans ran when commanded by OBD11, that means the wiring, ECU, fuses and fan motors are fine. Therefore what ever is commanding them to come on needs fixing, which is probably those AC pressure switches. If the AC system detects it has no refrigerant, it won't trigger the fans.
I think that's your issue mate. I think they are working in traffic jams, but you haven't heard them running. They're not loud fans at all, except as said before, when running at maximum speed, and even then, you need the window open to hear it.
Having said that, if they aren't working at all, because the engine coolant fans also have to go through the AC controller, that is an utterly dumb arse piece of design by VW!
Have you tried leaving the car idling at home until they come on? It can take quite a while, sometimes 10 mins or more.