I was questioned by french border police first time ever last year on my return journey from Morbihan. That was while queueing up in Roscoff for the ferry back to Cork. Both are EU ports.
First, they only wanted proof of ownership, nothing about VAT. Apparently, some yacht by the name of "Homer" had been reported stolen, so I was suspicious. As I had no proof of ownership with me, they took photos of my boat to compare with photos of the stolen "Homer". When the photos did not match, at all, they asked for an insurance docket, which I also did not have on me. Then they decided I did not actually require insurance cover for the boat for leaving France aboard a ferry.
Finally, they cautioned me not to return to France on own keel without carrying proof of insurance.
I took that to heart of course.