Dirk is correct. EU 465/2012 dictates that SOCIAL SECURITY has to be paid in the country where your base is situated. Usually the pilot is a director of an umbrella company which in turn provides services to Fr via Storm or Brookfield. It is the umbrella company who employs the pilot which has to pay the employers contribution.
TAXES are as per double tax treaty between the country of residence of the pilot and the country of residence of the umbrella company. These are international agreements which have priority over national tax lax and Italy can not change them unilaterally.