That's correct. As you can see on our pricing page, we charge additional fees for transactions made through gateways external to Shopify Payments. More information regarding processing limits and fund reserves here.
Shopify charges additional fees 2.0% on the Basic plan, 1.0% on the Shopify plan, and 0.5% on the Advanced plan for transactions made through payment providers other than Shopify Payments.
I hope this helps to clarify! Please let me know if anything is left unclear.