You're not actually intercepting the FCM's signal... you're basically bypassing the FCM altogether. I did a write-up for 6Tech many moons ago, but that's been gone a long time... don't know if the archives are still around or not. I don't own a 6 anymore, but I'll try to re-hash from memory best as I can. Please bear with me... I'm an ME, not an EE
I will refer to the stock fan control module as "FCM".
The power and ground for each fan motor passes through the FCM. The (+) wire is hot at all times (the fan motors always have full battery voltage)... the FCM controls the fans' operation through the grounds. If you splice into the (-) wire between the motor and FCM and connect that to a chassis ground, the fan motor will receive 12V (or 14.X volts if the car is running) and the fan will run at 100% speed. The FCM still works as designed, but you can use this auxiliary connection to power the fan whenever you want.
I suppose you could put some resistance in this line and throttle the fan's speed back, as long as your resistor was capable of handling the wattage. I think the fans drew roughly 15A each at full power, but I'm not positive.
I used a cheap Hayden fan controller (with the probe that sticks into the radiator fins) because I already had one... the controller just switched that auxiliary ground on/off. You could also use a toggle switch and relay, if you're not interested in any automatic function. I only connected one fan motor because both fans at 100% power was overkill, but you could also wire them independently (one on a controller, one on a manual switch).
I imagine you could use one of those PWM controllers you're talking about and actually have variable speed control. I've never tried it, but it seems like it would work the same way.
Hopefully that makes sense. If not I'll try again...