I feel your angst!
We are an Australian flagged boat that is VAT paid. VAT was paid by the previous owner and boat transferred to us in the EU (france). There is so much conflicting well intentioned advice on this forum on this issue for a variety of reasons and it had us very confused. Dave (Goboatingnow) has the best advice so listen to him.
It gets confusing as hell but since you ask here is our real world experience from 3 years in the med -
The VAT status of our boat has been checked only once by french customs when we had work done on the boat. We went to them. They had no problems with our status as VAT paid on production of the previous owners sales invoice showing VAT paid. They were pretty agro at the time too sending a vessel after a 60 foot lagoon
that had been sold vat unpaid from a german to brit - 230,000 euro bill for them- the very next day.
NB there are many who mention a VAT paid certificate. In France
at least this simply does not exist. As I understand it that is the case elsewhere also. Its a furphy. The proof of VAT status is the original sales invoice of the boat and then transfer documents from that owner to you ideally showing that transfer occurred inside the EU. Your boat is then VAT paid in the eyes of the revenue raisers.
We have NEVER been asked about out VAT status anywhere else in the EU including many trips to customs in France
in particular. Its just not on their check list for clearing in and out of EU which we have done many times now. Spain may be different we dont know. we spent a month there from France and never bothered to clear in, just like all the EU flagged boats moving between france and spain.
All that said I dont know why you would flag the boat non EU if thats where you plan to sail her and you have the option to do so. It means you can legally avoid clearing in between spain and france unlike us.
Dont sweat it. Many on CF get their knickers in a twist about all the boating
regs in Europe
such as VAT, competency etc but in reality in the main the officials are pretty relaxed about the whole thing and are often just as confused as everyone else on how to operate clearance procedures.
Now schengen thats a real hassel but you can avoid that one....