I cannot give you the exact wording in the regulations but the way I understand it is that the CAA can provide an exemption to the EU regulations so that these flights are possible. Operations with historic airliners have never really stopped in The Netherlands, Germany and Switzerland (those are the ones I know of).
The question remains whether the blame should be placed on the CAA or somewhere else. It may also be a case of Air Atlantique not willing to go through the motions needed. You might also want to ask this question at Duxford as Classic Wings has never stopped flying passengers in their Dragon Rapides,
AFAIK.
Dragon Rapide at Duxford