Ok it looks like I finally have some reliable info from a Honda technician.
The guy explained the technical details to me so I don't remember it all but this is the jist of it. Basically the reason, the Vario transmission gets damaged on CNG, is that the sensor tells the transmission to operate at one power level while the engine is at a lower power level because CNG produces less power per RPM. What happens then is that the transmission belt slips and causes a dent on the pulley. Then whenever the belt goes over that part of the pulley it causes a grinding noise.
He said that there is another type of sensor on the market (forgotten the name) that fixes the problem. It is an additional 15000 rupees on top of the usual CNG kit and that transmits accurate info to the transmission. He said that this sensor has been on the market for 6 months and he has not heard of any problems so far but obviously there is no guarantee for the future.
If anybody is interested in more info about the sensor I recommend you speak to a Honda technican at the Honda head office not at the dealerships. The head office in Karachi is on Karsaz Road.