I think we solved this here:https://community.shopify.com/c/Accounting-Taxes/Tax-for-Second-Hand-Goods-VAT-Margin-Scheme/m-p/1010461#M5062

I encountered this issue this morning. I was trying to set up a Margin scheme (products sold with 0% VAT) but Shopify only allow you do use a manual collection.  SHOPIFY, please allow us to assign tax rules for automatic collections. It's a nightmare...

No you don't need to charge VAT to EU customers. They are treated as Rest of World now.