This all hangs with KK's info above: the factory bolts came in with specific coatings that gave a consistent and predictable relationship between torque and clamp load (bolt tension).
the engineer schedules a torque test with fastener engineering... They get all parts and fasteners involved sent from the supplier or assembly plant that are off production tooling and processing... The engineer and fastener engineer meet one day and assemble the parts and twist the nuts and bolts until they break... (It's fun to break stuff - and get paid for it)... Lather, rinse, and repeat many times to get a good sample size to establish repeatability (capability)... Then the fastener engineer reviews the torque curves that were recorded during the testing and recommends the torque spec for that joint... That becomes the spec that the assembly plant will use and be held accountable to maintain...
There are also cases where they will also develop a spec for service to be published in the service manuals, realizing that most shops just use some form of torque wrench and not have special custom torque monitoring equipment like the factory uses...