Where do standard torque values in maintenance manuals come from?
The standardized values are related to the yield strength and elasticity of the fastner.  Bolts in normal tolerance holes are effectively spring clamps (bolts in close tolerance holes can be better thought of as spring clamps + shear pins) and when you are tightening a bolt you are using a spiral wedge, the threads, to force the bolt to stretch to clamp the parts together.  

You want to be able to stretch the bolt to apply as much clamping force as possible without exceeding its yield, or permanent deformation threshold.  It's like stretching a spring too far, so that when unloaded, it is longer than before.  You would say that the spring is ruined if that happens.  Same with a bolt. If you overtorque it and exceed its yield strength, it will be a bit longer than before when loosened and will have lost some of its ultimate strength after being permanently elongated.

So the standard torque tables are limits on how much the bolt can be stretched, converted to the equivalent rotational force applied to the spiral wedge of the threads.  The values are those that keep the axial tension force below the yield threshold, with some safety margin.  The standard limits are a function of the material strength and elasticity of the material that a particular bolt is made from.

A lot of the time torque values are given that differ from the standard values because the designer wanted to customize the clamping force for some other purpose, such as to limit clamping force on the base material or gasket or washer, or limit shear loads on parent material threads (like a steel bolt in an aluminum casting).  The normal engineering practice is to quote a torque value on the engineering drawing (and hence in the Maintenance Manual procedure) when it differs from the standard tables.

So as a general rule, when a torque value is from the standard torque tables, it's a limit for the bolt itself and is related to its tensile yield limit.   When a special torque value is given, it's a limit to control force applied to something other than the bolt itself for various other reasons.