I think the answer is you torque it the way they spec it. For engines they may say to lube the bolts first. It makes a big differance if you clean the bolts, and run a tap in the holes.
Some automakers went to a torque to yeald with a torque angle meter. First you torqued it in sequence sometimes in several steps to a higher torque each time. Then you put a an angle meter or gauge that measured the degrees of turn. A spec might be 20 ft/lbs, then 45 ft/lbs, next 90 degrees. The idea was to be more accurate of streching the bolts to the limits. Many times it was recomended to not reuse the bolts for this reason. It was a pain and not allways a good result IMO.
A torque wrench is never 100% do to factors like how clean the threads are, lub, liquid or material in a blind hole, was the bolt or threads streched too much before, thread condition. For that reason I have seen torque wrenches break bolts, strip threads, or torque a bolt before the head is making contact with the other surface. That's why it is up to experiance to help tell you that thing is not getting any tighter or is too loose. I'm not saying not to use a torque wrench, just to pay attention.
I used to joke that my arm was a torque wrench and I could measure the effort in grunts. Like you torque this to 1/2 a grunt (50 ft/lbs). Just as your eyes allow you to judge inches you arem can estimate torque.
