I think that there three ways to determine the value:
a) in case of a platform as eBay, the tax is automatically calculated based on the price. A code is added to the shipment, so that it is clear that the tax is collected and send to the country of the seller.
b) the seller has to fill in a customs declaration including details about the shipment and its value.
c) if customs considers the declaration to be implausible (e.g. "gift" and "1 €"), it asks the seller to provide evidence for the value (e.g. a bill and evidence for the payment). How c) is done, I have no idea. I know only that this happens, because I had to provide such evidence multiple times.