There's a difference in behavior between platforms that's worth understanding before you set things up.
Tiendanube
If you set up a custom payment method, the tax percentage you enter for that method replaces the store tax for those orders. It's not cumulative: one or the other applies.
Shopify
The store tax applies to all payment methods and can't be overridden per method. In Shopify you can only set fees per custom payment method, not taxes.
If in Shopify you need a specific method not to carry the store tax, the way to do it is to adjust the general percentage or offset it with an additional cost, not to set it per method.