This topic has converged mainly into a tax related topic, but there is another important reason "why" an EU citizen would register a boat in... another EU country.
Sailing restrictions in his own country.
I'm Portuguese (although not living in Portugal), but if I would like to own a Portuguese flagged boat and keep it there for my vacations "back home", I would have to be a holder of "god knows how many" licenses and in-between steps just to be able to get out of the harbour. Let alone going somewhere offshore
Portuguese licensing system (I like to call it a national "scam") went straight into the hands of private companies that charge a king's ransom for every single license
they issue... If someone would start from stratch and wants to go all the way up to "no limit cruising", it will cost them something like +2500 euros total and +3 years from step 1 'till the end. No more boating
for poor people with cheap boats and with wide horizons.
items obligatory on board... do not even fit into a small cruiser! And so on... And hey... the famous portuguese officials are famous for a reason, right? I was once boarded just for them to check the first-aid kit! And stories abound of fines being issued because one "band-aid" or "pin" was missing!
Registering it under, say Belgium or Netherlands
, avoids (almost) all of these restrictions, complications and expenses...
Long gone are the times where Portuguese sailors could sail out and explore new worlds...