No, The matriculation tax does apply to spainish residents, but that only kicks in after 180 days, ensure you dont overstay and ensure you can prove when you arrived,
Carry proof as to your ultimate destination
, letters of residence, utility bills. etc.
IN general they will have no interest in VAT.
You will howver need to register the yacht on a ships register as you will need documentation
. What register will you use.