Sophia here from Shopify. Welcome to the Shopify Community!
The charges and transaction fees that apply to each order on your store depend on the payment gateway used to place the order as well as the plan your store is on. If you're using Shopify Payments, you'll see a credit card rate deducted from each order in your payout, but additional transaction fees do not apply to your store's orders.
The transaction fee percentage you see on our pricing and plans page under "Additional fees using all payment providers other than Shopify Payments" is only applicable if you are not using Shopify Payments. Let me know which payment gateway(s) you're using and if you have any questions. I'd be happy to break down the charges and fees in more detail if anything is unclear.
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