From my experience, many of the flat rates are simply a percentage over the factory warranty rate. Problem is warranty often includes some additional addons for certain labor operations added to the main job. This is OFTEN overlooked by the motor guide and the others.
There are also certain jobs that they are way over the actual time that would have been charged by the dealer. Go figure how they arrived at that. Maybe because we know shortcuts that they cant figure out.
In any case, a labor guide is just that ... a GUIDE. Shops can choose to over ride it when there are obvious mistakes.. But dont bank on many techs giving you a break when the book is in their favor by a wide margin... just the facts of life.
In some shops they charge the minimum number of hours and pay the tech based on that. Then they charge a huge bloated hourly rate to cover thier butts, leaving the techs eating the loss.