I am a Turkish citizen who is holding a Turkish Passport and a GNIB card for Ireland as I am married to an EU citizen.
I have a similar situation as you had. I would like to fly from Hamburg-Stansted-Cork/Ireland. Normally, I flew before via Heathrow with my card and together with my spouse, however I am not sure about Stansted airport as there is no transit area.
Did you fly without a transit visa via Stansted to France at the end?