I don't know WTF the are doing with VAT, but UNLESS the have a VAT number in each and every country they charge a different rate for, they have to charge the Swedish VAT and declare it in Sweden. They OBVIOUSLY need to state their VAT number for the country they charge the VAT for. They can't charge 19% for Germany and have their Swedish VAT ID on the invoice.
If they don't follow protocol, they risk ending up in a world of hurt.
As far as I notices during their ordering process, they ask for your VAT-Tax-No. and if you have one, the invoice is issued without VAT. If not, they tax swedish VAT.
Everything seemed to be accurate.
No, this is not right. This is only right if they want to stay under these thresholds posted much times. But if they sell only 19 jupiters to germany for example
they are not allowed to use swedish vat.
http://ec.europa.eu/taxation_customs/resources/documents/taxation/vat/traders/vat_community/vat_in_ec_annexi.pdf
These thresholds only apply to distant selling (shipment directly to consumers), not for pickup in Sweden. And they don´t apply, if the buyer is a VAT-registered company. If the buyer has a VAT-Tax-No. the invoice will be free of VAT. In this case, the seller has to check the VAT-No. and needs proof of identity. We often buy large quantities of goods form other companies within the EU (single orders beyond the German threshold of 100.000 EUR) and never pay VAT. But we have to declare these buys monthly to the German tax-authority.