If someone buys your product for $100 and Stripe's fee is $3.20 and you issue a refund to someone you will refund the user $100 and Stripe keeps the $3.20 so that refund really cost you $3.20.
If you had a deal where you were directly exposed to all the fees involved, what I'd expect is that you net fee on a transaction would be composed of fees from three different categories.
1. Per transaction fees that apply to both charges and refunds.
2. Fees proportional to the charge amount that apply to both charges and refunds.
3. Fees proportional to the charge amount that only apply to charges.
On a charge you'd pay the fees from all three categories. On a refund you might get back the fees from category #3 you paid on the charge, but you'd again pay the fees from category #1 and #2.
For example if you sell an item for price P and the fees from the three categories are F1, F2, and F3, your net gain on that transaction is P - F1 - F2 - F3. A refund transaction has a net gain of -P - F1 - F2 + F3. That would bring your total net for the combined charge/refund to -2 F1 - 2 F2.
This we should expect some net fee for a charge followed by a refund. For small transactions that net fee could be up to almost twice what the fee was for the charge alone.
Most processors though don't directly expose you to all the fees. That's because there are a bazillion different possible fees with each different subsets applicable to any particular transaction. So most processors expose a simplified structure based on averages over a large number of transactions across similar merchants. Most merchants prefer that.
When doing such a simplified fee structure, they could set charge fees based on the average for F1 + F2 + F3 and refund fees based on the average F1 + F2 - F3. But refunds should be much less frequent than charges, so it seems find to me when doing a simplified fee structure to just average the refunds in too, and just deal with fees on the charge side of things.
Your information is outdated. PayPal keeps the fees now. https://www.theverge.com/2019/9/20/20876570/paypal-refund-fe...