Experienced the exact same issue on my 2018 RS3. I could hear it while driving in heavy stop and go traffic. the dealership replaced the whole back muffler piece. but it came back after a while. I learned to ignore it after a while and knowing it was the flaps opening/closing.

I'm new to Audi and the biggest issues I ran into, ranked from Safety to annoyance:
- Tires. Day 1 issues with Pirellis. 2 of them blew out driving in the shitty streets of NY. Paul@SupremePower hook me up with a set of rims/tires and have never looked back. zero issues

- Driver malfunction/low fuel rail pressure/limp mode - Numerous visits to the dealership and no fix. Happens on heavy stop and go traffic (hour or more for me). Slowsedans posted a great article/thread as to likely root cause and why this happens. I have to get around and do the suggested logging to make sure my issue is not from a weak/defective factory fuel pump (unlikely)

- Exhaust Squeak discussed above.

Outside of the above quirks I love this car. Everything that I wanted (Go fast with Class, etc). I just hit 14k miles and ready for a tune.