What was happening was that collection was being done by the customs, and only a small fraction of the goods were being flagged for not having VAT, then they had to collect it, and then proceed to return it. This puts an extra layer of work on customs, and many goods are sold at a price that can't be matched by EU businesses because they have to collect VAT.
So EU now demands businesses that want to do business in the EU to do what every EU business does: collect VAT on sale and return it.