I can only think there are some programming errors in the websites Some coins are being dealt with on the marginal rate scheme whilst others are having full VAT slapped on them, there were silver Krugerrands with 0% VAT on aurinum.de. So it looks like people are being sloppy and there are errors in the websites. I think quite a few sites are a bit sloppy, so just buy at the best price and to hell with it.
I'm not a vat registered business so don't know the mechanics of it but it seems to me that what you say is correct only from the business viewpoint. The customer pays vat on the total selling amount, which is the desired, from Government perspective, effect. Don't forget that the original seller, the manufacturer or wholesaler, will have paid vat on the first sale as well. This added to the vat difference you speak of will mean the Government gets the vat on the full retail selling price.