Haven't had that direct experience, however I did install an RNS510 in a Superb with factory amp and had a somewhat similar problem.
Basically although the car was correctly coded for 'sound system' there was no sound. In my case the amp had sort of gone to sleep due to the original Bolero head unit being removed. I had to do a scan for fault codes on the amp and it came back to life.
In your case I think that you may just need to change the coding. You may need to set the coding up. Trial and error maybe.
Try this for starters:
Volkswagen RNS 510 coding when installing with a factory amplifier | my-gti.com
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