The new head unit is responding to the CAN commands on the infotainment bus same as an older unit at address 56 would. It can see a signal for mute, reverse, volume up etc.
There is no handshake as such in CAN. Just messages on a series of buses which connect and are filtered via the CANbus gateway.

I've never actually actually done any work with a Composition Media unit. I am only making assumptions based on what works in Discover Media.

2 ideas: It may be that the PDC messages are not being passed by the 3c8 gateway correctly - this is easily confirmed by testing with the 7N0 gateway in place.
Failing that it may be that you need a 1k8 PDC module like the Composition Media unit is supposed to see in a factory configuration like in an MY16 Jetta or Tiguan...