The VAT is payable at the tax rate of the first port within the EU that you clear into. I believe that the VAT rate in Croatia is 13%, which is less than other places. I would have expected that one could find a method of valuation in Croatia, perhaps involving payment of "fees" sans receipt, which might minimize the valuation. It is unfortunate that you weren't able to take advantage of last year's reduced VAT registration fees
that Croatia was offering, that would have saved you a significant amount of money
My boat is also not VAT paid and I would like to minimize my tax liability once I enter EU waters. I believe that the Germans use a linear depreciation model which penalizes newer boats, as their true value is less than that used in a linear model. It is difficult to value boats, since there's no official "blue book" value and there is a large difference between online asking prices and actual sales prices.
I think that your best bet is to use whatever contacts you can find in Croatia to negotiate your VAT payment there rather than in places such as Greece
and the U.K.