That's why I'm fretting. If I intend to sell it for the equivalent of $3.99 and screw up the VAT, I could be selling it for less.
Smashwords handles VAT the way it should be done, by having you sign in before you see the price of a book, and they add the VAT when they list the book.
Amazon is interested in sales, and by listing books without any regard for the final price, they're expecting authors to eat the taxes. If they don't, they'll often take the fall when the books don't sell as well. In short, it's a bad deal for authors.
The key with book sales, from all statistical evidence, is that pricing is essential. Ending prices with .99 denotes that a book is cheap (inexpensive). Even figures denote quality, when .98 conveys different messages. But adding a specific VAT amount screws up this type of pricing scheme.
Your best bet is to either ignore the VAT entirely, or bounce the price up a full increment (4.99EU instead of 3.99EU). Depending on the price conversion, I'll either eat the VAT or increase it, but most often I'll boost it to fit the pricing model.