If the goods are held at the non-EU seller’s location, then the goods have to first clear through EU customs. The seller can do this when the goods arrive at an EU country for the first time. They can pay the import VAT and customs duty to bring the goods into the EU for onward delivery to their customer. If the seller wants to reclaim the import VAT, then they must VAT register in the country where the goods are being cleared. Otherwise, the seller must absorb the import VAT as a cost, as well as the import duty.
Alternatively, the non-EU seller can force their customer to settle the import VAT and customs duty. Typically the delivery agent will charge the customer this amount before they hand over the goods. Whilst simple, this does often deter customers from repeat business with sellers.