I started out my automotive software career with Ford, and as part of the new college hire training program, I actually got to see the process of how "book rate" is determined. They take a brand new car, straight off the assembly line and give a master mechanic a process sheet (head gasket remove and replace, for instance). He has a tool cart with a computer next to it, about 6 feet away from the vehicle. For each step he starts a timer on the computer for that step, picks up the necessary ratchet and socket or whatever, loosens the next bolt, walks the ratchet and socket back to the tool box, puts it away and then finally stops the timer. He probably practices the procedure a few times before the timed run, but basically this prevents the company from setting the time to do a job super crazy low.

He's also not allowed to take any shortcuts from the book procedure, which there frequently are a few available (use a long wobble extension bar and a universal joint and you can get in without taking off all of the stuff above that bolt, whatever). On the other hand, this is the warranty rate (meaning new cars, largely less rust, etc). Independent/non-dealer mechanics will typically charge more time than the warranty time estimate from the manufacturer to account for things like rusty vehicles with harder to remove bolts and such, though this is usually in the rate book they subscribe to from whatever information source they pay for (warranty + 20% or so).

The issue is that the estimated time for a job is probably a high estimate for a brand new car and probably a low estimate for a several year old car, and the risk of that is on the dealership. The dealership then pays mechanics an hourly wage ($20+, fairly high for well certified master mechanics) and assumes that the hours listed on the job from the manufacturer are accurate, leaving the mechanic to take the risk if it goes over. Generally, the dealership loses on this proposition too, since they lose out on business/bay/electric/heat/etc for the lost time, so they don't like warranty work. They can upcharge/charge for more time/etc on a job for a customer, not for warranty repair due to contractual obligations to the OEM. This is particularly bad for Ford, since they currently lead the industry in recalls and warranty spend, meaning that their dealership networks are getting a lot more of that kind of work with limited profit and no ability to turn it down.