dirk,
you forgot to mention one thing of para. 14.3: INTERNATIONAL OPERATIONS.
I can guarantee this is being looked into by a pool of legal people with "powerful" connections....
And there are other things you forgot to mention like the effective place of management, with 40 aircraft and crews permanently based in Italy it will be hard to prove you are just "passing by".....and remember that if it was like FR claims then every airline would move their offices to Ireland and happily operate in Italy,Spain,Germany,Sweden etc. enjoying irish tax benefits.
Another thing is social security, you seem to know your stuff so please explain how in practice you can pay social security in Italy from say your Irish/Maletese/Cypriotic company.