Another part would be import duties.
Zero% pretty much everywhere in Europe on computers and software.
The price difference is a result of multiple factors. Taxes (not just VAT), import duties, exchange rates & a generally higher cost of doing business.
VAT is not a flat tax. It is exponential, meaning a 20% VAT on two different products sold at the same price may result in different total amounts. Products are taxed at every level where value is added. Consumers don't see this and cannot calculate it on their own unless they have an intimate knowledge of the manufacturing process.
Irrelevant. These things are not manufactured in Europe. There is one instance of VAT slapped on these things and that is the input rate on the finished article on import into the country. This is offset by the output rate collected on the retail price in each country where it is sold.
The other factor is the higher cost of doing business in the EU. Apple is very careful to ensure pricing is equal across the board (with very few exceptions) in a given market. Retailers need to be able to sell their products for the same price that Apple does. This means that their higher costs must be factored in. Employees in the EU are paid more than their counterparts in the US. Taxes are generally higher (as are the benefits that most citizens receive) as well. Real estate is usually more expensive as well, and carries its own set of taxes.
Whatever the average EU citizen pays in taxes, the average American has to pay by way of health or education plans. Things cost and don't occur in a vacuum. In short for all the taxes Apple pays for its European staff, it has to compensate its US staff directly in wages. The average wage in the US is not as low as it is in Portugal, for instance.
Real estate in the US can be astronomical, too. Particularly in the marquee sites in large cities that Apple prefers.
The main cost difference appears to lie in the better consumer laws in Europe, but these only really affect those companies who produce shoddy products that need constant repairs, replacement or refunds. I would be surprised given how much Apple trumpets its customer satisfaction rating that Apple is particularly afflicted with this. It doesn't explain the big mark ups that Europeans et al have to bear after taking tax etc in consideration.
Other US companies, like Dell don't seem to have to gouge as much and its operating model is not a world away from Apple's. Manufacture in the Far East, flog everywhere else.
Apple is profitable and fashionable at the moment. That is why it does what it does. Because it can get away with it. That is all the justification it needs. Apple is not your mother, brother, friend, or anyone who cares about you. It is a cold, business organisation which is only interested in creating wealth for its shareholders. The minute you stop paying for its products is the second Apple stops caring whether you exist or not. The quicker people recognise and remember this, the better.