I fly an ASG29 which has carbon cockpit.
The carbon is definitely an issue for the flarm antenna hence the reason for mounting on top of glare shield.
The Transponder signal is much stronger and as such the carbon is not as much of a factor. Your range below maybe reduced but should still be plenty. Most pilots reduce the PCAS range to 3-5 miles which is way below the range you will get. Mine is partial below, the top sticks out above the glare shield through a hole and the reception is more than enough. I did not experiment with the antenna fully enclosed under the glare shield.

Ramy