We have had this discussion previously and this resulted in information about a unit called SOLVIT coming to light. SOLVIT does not make a lot of noise so you may never have heard of them but here is what I wrote last time we delved into this topic.
SOLVIT is a problem solving network in which EU Member States work together to solve without legal proceedings problems caused by the misapplication of Internal Market law by public authorities. They are part of the national administration but, not being a court, they are no more than arbitrators (although not in a legal sense, i.e. not a court of arbitration). SOLVIT is an informal approach to problem solving and, to my way of thinking, a great initiative greatly cutting down the costs and time involved to have a case resolved in court. You cannot win or lose a case with SOLVIT. What matters though is that SOLVIT can lend weight to one's argument hopefully that is sufficient for an authority to change their decission in your favour.
There appear to be two sailing vessel related cases in which SOLVIT assisted in resolving the problems:
The first, as you mentioned, was the Frenchman's case.
The French owner of a sailing yacht registered in France was asked by the Portuguese authorities in Porto de Sines to register his boat in Portugal because he had stayed in Portuguese ports for longer than six months. The yacht owner wanted to keep the French flag and turned to SOLVIT for help. SOLVIT Portugal contacted the maritime port authority to clarify the situation. It appeared that the six month limitation was not applicable to EU registered boats. This was explained to the local port authorities so that the French sailor could keep his flag
The second involved a German charter business.
A German enterprise charters four yachts under German flag to tourists in Italy. The business-owner was fined for not having registered its commercial yachts with local port authorities according to recent Italian regulations. Five months later, after repeatedly trying to obtain registration, the business-owner was told that registration would only be possible if the business was established in Italy. SOLVIT Italy stepped in to clarify that this condition was not in line with EU law and that the authorities should accept the registration in the German Chamber of Commerce. All four yachts were registered and charter licences were issued.
SOLVITs intervention in the above instances is, for European Union sailors living in another EU country, really positive. I think there is a very good chance that Spain will also be "encouraged" to follow the recommendations SOLVIT made in the above cases.
Aye // Stephen