So, after having gone through hell to take out of Italian custom my Italian registered scooter, I list here some numbers in case any of you would like to do the same.

Shipping was from Bangkok, Thailand to Genoa, Italy.
I couldn't take the bike in Genoa as I sent it with a LCL mode so 90% the container clears customs for the whole content in Milan. So I had to pay for the unloading of the container from the ship and the consequent forwarding to Milan. Again I couldn't go and take the bike from the coloader warehouse or, as told by them, it would have been more expensive than having the scooter delivered elsewhere in Italy.

I was asked to give the Carnet de Passaage in order to have it cleared with an extra cost and I had to use legal articles to prove them wrong (ie carnet de passage not be used in the country of residence plus only the issuing organization can clear a Cdp).
I was asked many times for the invoice of the goods and the PRA registration (the equivalent of the DVLA) and I had to explain them via many phone calls the uselessness of their requests.
Eventually after a week of exchanging phone calls I solved the issues and I had the scooter delivered to and address in Milan.

Total cost paid in Thailand for the shipment Bangkok to Genoa (without ocean freight): 330€.
Total cost paid in Italy for the service (inclusive of ocean freight 63€): 782€!!!

I strongly advise to any countryfellows or any other biker willing to ship their bike to Italy not to do it! Apart from the level of incompetence shown to me by the freight forwarder, the inbound costs are much higher than other EU contries and definetely less troublesome in terms of bureocracy.