I know that A3 is loath to wave their booking fee, and booking two seprate tickets was quite the upcharge.

So I ended up using booking.com, because they offerd Flex and ComfortFlex. (While I can change the currency for hotel bookings, I needed to use a VPN to get the flight charged in Euro.) Furthermore, I need accommodation on Chios, and after booking the flight through booking.com I obtained an additional small discount towards my accommodation booking. (The discount was 15%, but I get 10% anyway through their "Genius" loyalty program.)

Afterwards, I was able to add my A3 booking to my Miles&Bonus account using the A3 app. (I could not figure out how to do that on the A3 website.)