Interesting input.
IMHO you should have landed and sorted out the PNR vs PPR snafu safely on the ground.
I did wonder, and if it happened again I would probably declare a "low oil pressure" mayday and land. In this case we diverted to Treviso, whose ATC said they have avgas, only to find aeroclub-only avgas there. Eventually we filled up across the Alps in Germany.
If you were coming in from abroad like you imply, then there was an ATC flight plan, and to me that is yet another indication of the fact that you were going into LIPU.
Sure they knew it, and I know they knew it in good time, but somebody either messed up or they wanted to teach us a lesson. We flew in from Croatia. Unfortunately, flight plans are almost universally disregarded for PNR/PPR purposes. The only airports I have come across where flight plans are thus used are some H24 ones (Prague e.g.) where the handler organises things according to the incoming FPs popping up on his PC. But Customs are not an issue there; all H24 airports I know of are H24 Customs anyway. Some big ones do have PPR though.
More recently (August) I flew to Caglieri (from the UK, direct) and it was very smooth. A complete contrast to the rest of Sardinia. Not really cheap though
Alice is an ISP in Italy but I don't see the link with the PPRuNe forum...
I think there was an infected link on that URL.