Following up on the EU VAT thread...

There may be a higher authority to refer to, but Customs at Lefkas and Messalongi say that, to quote (from Lefkas)…. “We can be signed out of Schengen and onto the transit log for 6 months”, thus avoiding use of Schengen days.

Also, contrary to 'common wisdom' there is no requirement to sign in and out of intermediate ports unless changing conditions of transit (E.g. crew change), only to have the TL on the vessel for inspection.

It would appear that the ability to do this is available to signatory countries to the <THE CONVENTION ON FACILITATION OF INTERNATIONAL MARITIME TRAFFIC, 1965 (Resolution FAL.12(40)>. Searchable on Google.

The rules on this particular practice are optional (‘Recommended Practice’ in the FAL). Not all countries adopt these rules. I suspect Spain, Malta and Italy do.