In Spain, comisión commonly means a bank fee/charge, e.g. a fee for a transfer, maintenance, withdrawing cash, etc. It’s not a “commission” in the salesperson sense here; it’s a service fee.
Spanish uses the present tense after si to talk about real/likely conditions in the present or future:
Here si clearly means if because it sets a condition: they charge a fee if you do it at the counter. Si can also mean whether (indirect questions), e.g. No sé si viene = I don’t know whether he’s coming. The structure tells you which one it is.
Spanish commonly uses en to express the “place/method” where a service is done: