Everyone is right but the sting in the tail is highlighted by pauln90 - no factored parts. And how do you prove the non franchised garage did the work to the specified standard?
Having said that I bought a BMW 520 (2nd hand) about 10 years ago. There was a BMW warranty for 12 months. After the first service at the local BMW franchise I was so disgusted I took it to a local back street garage for the next service, sacrificing the warranty, and I have taken it there ever since. It still goes well and I am certainly not tempted by the scrappage scheme.