I believe I’ve always paid back just my proceeds, but I seem to recall that the developer agreement does allow them to retain the commission. Maybe they only exercise that option if they think you are doing something fraudulent, or something.
I don’t think there is anything in the financial reports that indicates when the original purchase corresponding to a refund was made. You just see, for each period, the number of sales and the number of refunds. You don’t know if those refunds are for purchases in the current or a previous period.
I believe that the refund policy may depend on where the user lives.
Your accountants are no doubt concerned that they cannot consider payments from Apple “final” until any potential refunds have been accounted for. It is their job to worry about this. But frankly, your concern should actually be “is my app so terrible that lots of people will ask for refunds, and Apple will agree to grant them?”. If that is a real concern for you - find another job! Some small level of refunds granted to “idiot customers” who genuinely pressed the wrong button or didn’t read the description are normal. You will get a feel for what percentage that is for you after a while. I think mine might be around 1%, but I’ve not checked recently.