just some clarifications
The Schengen agreement is an EU agreement, it was "adopted" by the EU. But simply because its an EU agreement doesn't mean all EU countries adopted it. ( This is true for many EU agreements. various deals, horse trading etc, mean degrogations from all sorts of EU agreements get handed out like confetti.
The second thing to bear in mind , off all the countries to clear into , Portugal
is by far the worst bureaucracy in the EU in my experience, followed by the Greeks. Its full of petty officials that in fact often know little about the facts. I was asked recently about a boat requiring a TIR ( which has no meaning for a private vessel) because he had been required to produce it in Portugal
Ive run foul of them several times and Im very selective where I dock
BTW, its worth pointing out that paying of VAT in the azores
is not necessarily the correct or legal
thing to do for anyone importing a yacht into the EU, funnily the officials there will happily take your money
and not inform you as to the fine print around VAT and "new means of transport".
I know of several incidents where obscure rules, mis-informed officials etc have caused lots of grief and unnecessary worry. Unfortunately challenging these nincompoops isn't easy.