My car only had the first service done at Honda. The rest have been with specialists. I only got asked when it was last serviced and it was all approved.
Mine's a 57 reg and was done last September, inspected in August.
It's not just a roof respray, the rubber seal needs replacing with the revised one so it doesn't do it again.
The warranty work is guaranteed for the life of the car, so it is worth persuing with Honda.
If you don't get any joy trying again, go to another dealer. Honda UK will approve the work as long as the dealer sends off the proper supporting evidence. It helps if you have a good relationship with the service manager, but be polite but firm.