Tolerances serve to define the maximum deviation from the nominal value that will still allow proper function. Tighter tolerances do NOT mean a higher quality part, just a more expensive one. A part that is designed to accommodate a wider range of variation is less likely to fail due to things like contamination, thermal expansion, wear, and repair methods. Tight torque tolerances in a torque chart should be a warning to the mechanic that the joint is torque critical. It should be a warning to other interested parties that there might be a design problem.
The design establishes the tolerance limits but the tolerance specifications are not based on what the design requires or what the engineer wants; but what he can get. If the tolerance specification cannot be met, then the design is flawed.