You may want to look at it this way...
Flat rate times theoretically are times that an average tech would take to perform the work requested barring unforseen problems. A more experienced tech should be able to complete the repair quicker than an average tech. Most technicians are required to purchase their own tools. As a rule a more experienced tech is better equipped than an average tech. Many techs, if not most, get paid by the job and not the time involved.
Long story short? If you were charged less, the tech that takes his career seriously, has a better than average assortment of tools, would end up making less money for the job than an average tech. Wouldn't be much of an incentive to perform better would it? And, what if an average tech took longer and had no unforeseen problems... would you have expected to pay more for the work performed?
There are pros and cons on pay structures and they all have their own drawbacks sad to say because so many human beings just don't want to put out the effort that a customer deserves. Motorcycle dealers and/or technicians are no different. And, in fact, a good technician will spend substantial personal time getting better at his trade. If you look at your own workplace I'm sure you'll immediately see what I'm talking about.
Yes, a sad statement about employees in general.