I have a friend that took a John Deere road grader to the dealer (likely the same one as nutfarmer) in Oregon for a transmission repair. The bill was over twice the estimate, and took several months longer than promised. I believe that this is established policy.
On one hand, the manufacturers are consolidating dealerships in broad territories. This amounts to geographic monopolies. Geographic monopolies have become a way to control markets, and it extends to every level of business, possibly excepting retail. For example, in the mid-20th Century, Safeway grocery stores targeted small communities that could only support one supermarket. They would build a store in that town, hold prices down until the competition gave up, and then raise prices to throw off the cash to repeat the process in the next target. Quarry rock, sand & gravel, and concrete are commodities that are heavy and uneconomical to transport very far. National and multi-national companies have bought up the smaller producers and done like Safeway, raising prices for construction in the process.
Dealers on the borders between these local monopolies are loath to compete on price. It may be "professional courtesy" or just because they see no reason to give up the easy profit.
On the other hand, dealers have to hire from the available pool of wage workers. The best workers gravitate to private jobs at companies doing their own work and willing to pay the workers some of what they save on parts and dealer profit. Therefore, the dealers tend to have less productive workers, and the billing reflects that. I started working in Aviation in the early 1970's, and soon observed that no one made money in that sector until they moved their maintenance in-house.
I agree about the Service Managers. I had one experience where I was charged a core charge for a brand new clutch for a heavy truck. I ended up having to go to the shop owner and he almost made me threaten a fraud lawsuit before agreeing that the new clutch did not include a core charge. I'll bet they got away with that scam many times!