Tightening nuts is a subject which always creates much debate and disagreement resulting in confusion and the potential for damage to occur when poor practices are used.
In the engineering world the majority of fasteners are used to clamp the faces of a joint and prevent any relative movement by reacting the forces being developed during use.
Measuring torque accurately and repeatably is only one aspect of the problem as high levels of friction tend to generate low levels of preload which can impact on joint integrity as the preload developed may not be adequate for the application.
In the case of cylinder heads the external force may be axial and in the case of a wheel the force may be torsional.
In every case the joint relies on the preload or tensile stress developed by the bolt during tightening to clamp the faces of the joint together
The ideal method for measuring preload is to measure the stretch developed during tightening but this can be difficult to achieve with a stud although modern ultrasonic 'stretch' gauges are becoming increasingly common and can deal with this problem.
The least accurate and repeatable method for determining the tensile stress developed in a bolt is to measure the applied torque and this has lead to various approaches being used to improve the situation including the experimental determination of ‘nut factors’
http://www.hexagon.de/rs/k.htm
If we look at the typical losses that occur when we tighten bolts it should be clear as to why ‘torque’ tightening is a relatively poor method and can result in problems. A variation in preload of +/- 30% is quite commonly reported when using a simple torque measurement and I would tend to believe that this is a conservative estimate as it generally doesn’t consider the ‘operator’.
The figures above also assume clean and undamaged threads so if we take this type of problem into account the variability in preload just keeps on increasing.
The impact of lubrication not only tends to increase the preload for a given torque but it does reduce the scatter in preload as it tends to produce more consistent coefficients of friction.
So where does that take us?
I would say that the Workshop Manual suggestion is that only the dome on the nut needs to be coated with Moly grease as the frictional loss produced by the dome is likely to be greater than the 50% of a standard nut face and could result in more variability if these faces are dry.
Aluminium does also have a tendency to gall more than steel
I have to say that I would tend to use a light oil on the stud threads as they are easily strong enough to deal the small increase in preload that could be developed compared to a dry thread and would tend to reduce variability.
There are other issues which could be discussed and these would be the finish on the bolts and these will vary depending on whether or not bolts are phosphate or zinc plated.