Reconcile.ly lets you choose which account various income streams get mapped to. This lets Xero keep control over calculating tax.
If we see an item has tax included from Shopify, we will code it against your nominated Xero account for taxable sales. This lets Xero calculate tax at the correct rate.
So, it's worth making sure your order taxes are correctly set up on your Shopify Admin settings and that you're mapping to the correct Xero account.