I had a similar situation last year and my GP in Dublin had no issues filling in the SW form, even though the surgery was carried out in Cork! Charged me €15, but took me at my word when filling in the form (didn't ask to see any of the hospital or consultant documentation I had brought with me).
I was late submitting the form as well, and there's a section on the form where you can explain why. Payment was processed a few weeks later. Mine was paid to my employer, so you'll get a little slip of paper in the post stating the amount paid and for what dates. I didn't know what it was first because other than Dept of Social Welfare and the dates and amounts, there's nothing that indicates it's relating to the sickness benefit claim.