When you enable VAT calculation, we just calculate what portion of the total prices paid would constitute VAT, so VAT is already included in your gross revenues (e.g., in your PayPal account balance if you use PayPal for checkout). This calculation occurs when we process the order after the buyer has already paid you in full at checkout.
It's up to you to file and pay for VAT on your own, out of your own pocket, using the records we provide in your Transaction Log. As far as we can tell, sellers outside the EU can file and pay all EU VAT with any single VAT MOSS in the EU, such as the UK VAT MOSS, which would then redistribute any VAT due to other EU nations. That said, we're hard pressed to fathom any actual consequences that a low-volume seller operating outside EU jurisdiction could be made to suffer for failure to pay VAT on sales of digital goods to EU buyers.
VAT only pertains to purchases by buyers located in the EU, so buyers outside the EU would not see anything related to VAT in the course of their purchase. If you'd rather just block sales to EU buyers to avoid any VAT concerns at all, you can enable Shipping/Buyer's Address in the settings of each product, then go to Seller Admin > Cart Shipping Settings, specify your country and ZIP code, then in the Shipping Destinations list select every country you're willing to sell to*. Then click Next to apply changes and proceed to the following screen, where you can disregard any settings there and just click Back to Admin. Make sure you're using your E-junkie Add to Cart buttons (not Buy Now buttons), as this method restricts the countries available for buyers to select in your shopping cart.
* When selecting Shipping Destinations, if you're willing to sell to any country outside the EU, click the first country in the list, then scroll to the end, hold down your Shift key and click the last country in the list to should select everything; then hold your Ctrl key (on PC) or Command key (on Mac) and click each EU country to deselect them (see https://en.wikipedia.org/wiki/EUStates for a list).