I think we might be making this subject harder than it is.
You have to make the customer happy- that's all there is to it! As anyone who's been to aa auto shop knows, the way the bill is presented can turn a happy experience into a fit of paranoia, with everyone left miserable!
You look over a job, checking for differing complications. The you give the customer a price, which he accepts or declines...that's 'flat rate', as I see it.
Sure, there are "cheat sheets" that cover the most common jobs...but in the end, the result is the same. The customer is simply tols "I will do this for $XXX."
Contrast this to the "time and materials" method. The customer agrees to the job, without having any idea what his cost will be.
He gets your bill. The first thing is that he sees a charge for time over and above the time you were actually there. Parts run? Prep work in the shop? Padding the bill? He has no way of knowing.
He looks at the "materials" portion. %4 for a box he see at Home Depot for $.83. What's with that? And why did you get the $12 GFI instead of the $8 one?
Lets face it, a T & M bill can be very aggravating- unless there is a LOT of trust between the two of you.
With 'flat rate,' the job is done, the bill is for the expected amount, all is happy. That's why it works so well.
How you reach your particular price is a whole 'nother thing....
