If it really bothers you that much, just make a purchase and ask for a VAT receipt (if it's on Easy UK), which if they are charging vat, they are legally required to provide. However, as I believe that in the air, they are outside of the VAT rules, as said above, they can charge any figure they want.
Additionally, whatever the rules may say, businesses do make agreements with HMRC based on pragmatic approaches to simplify administration, especially where a company has to potentially account for several VAT regimes and contradictory rules as part of their normal operations. My experience of HMRC is that they are genuinely practical and seek solutions that are fair to the Govt, the taxpayer and the business, which minimise bureaucracy