You should be able to make the customer tax exempt, meaning they won't have to pay VAT. I use Seonids add-on to do this automatically, it also checks the EU VAT number.
Not exactly. Most of my customers are from the same country as I am (Denmark.) So in my use case tax needs to calculated for both my B2C and B2B storefronts. The difference between the two is that the first needs to have prices displayed with tax and the second needs prices displayed without tax. Taxes are still applied to both on the invoice.
Ah so you are talking about how it shows on the storefront? Can't you, for your b2c storefront, uncheck the boxes like: Display prices with taxes on category/product pages if the method of calculating taxes is based on a unit's price ?
Well, I just looked a little into it, and I think it might be possible for me to use the same tax method on both storefronts and then manipulate the price appearance through the templates.