First and foremost....... It's not the where, it's the who.
I have worked for both dealers, and independants.
The level of ability varies widely. If you were to visit the Toyota dealer where I work, I may work on your car,(30 + yrs experience), or the new lube tech guy may get it(good luck).
There is a MAJOR BENEFIT, especially with today's complex cars, of being FAMILIAR WITH THE PRODUCT. Much diagnostic time is lost/wasted/parts changed, because of this fact, at independant shops. This "EXPERIENCE" can actually save you money, vs an independant.
Do I NEED to mention TSB's,The latest hardware/software, updated parts, factory information and support.
Many times, without a TSB, the best tech in the world, won't be able to fix your car, if he doesn't know(and have access to) the latest software calibration for your car because it doesn't run properly all the time.
Many times, I am personaly amazed at the lenghts the management goes to, in doing the RIGHT THING for the customer (lots of freebies).
You should also know; If the dealer gets a poor CSI score(customer satisfaction index) directly related to customer mailer responses, ALL the management/service writers,etc, will loose their bonuses if the scores are poor. SO DOES THE DEALER PRINCIPLE.
Many dealers don't deserve the poor publicity from years past.
And yeah it sounds like you paid a little bit more than I would expect...but is your car prone to rusted/siezed/breaking hardware/ bolts, etc that the dealer knows will likely be a problem on older/high mileage cars like yours.???????
I wouldn't be happy paying that bill.