It's a good point to bring up. It depends on how long you intend to keep the car as I assume you want the history up to date for resale value??
My father bought a Porsche 944 turbo with 16000 miles on it and the service charges from Porshe were ridiculous, he found a well respected local co. who had built up a good reputation over the years for servicing Porshes....he took it there as it was much cheaper. He sold the car for book value later with no problems as the co. was known and respected and his book was stamped obviously.
The problem with dealers is the hourly rate is v. expensive for the same service....
I guess you need to think about when you will sell the car and what it will be worth when you do. If you keep the car for a few years and book value is only a few grand at that age, was it worth shelling out thousands in dealer costs???