Tmoose,
You correctly point out that overall joint design is important for maximizing the fatigue life of a fastened joint. But I would disagree with your assertion that the underhead and thread root fillets are not of much benefit. With your example of conrod bolts, the underhead and thread root fillets represent points of stress concentration, commonly referred to as Kt, which can be as high as a factor of 3 or 4 in an analysis.
The conrod bolts, preloaded or not, only experience varying tensile loads for each fatigue cycle. The tension loads due to piston inertias simply relieve the bolt preload strain and don't add to it. This equates to an R value between 1 and 0. The R value is the ratio between the maximum and average fatigue load. A properly preloaded conrod bolt would have not experience an R value above about 0.5. Much less of an impact than a typical Kt for a bolt or screw thread.
So the most beneficial approach to optimizing your conrod bolt fatigue life is to minimize Kt (stress concentrations), by using large bolt underhead and thread root fillets, by using mechanically rolled underhead fillets and threads, and by using conrod bolts with a long and reduced diameter shank body.
The improvements in fatigue life provided by mechanically cold-worked surfaces (thread rolling, shot peening, fillet rolling, etc.) has been shown to provide an increase in fatigue life of at least 300 or 400 percent. Just take a look at the specs for any high performance aircraft bolt.
Regards,
Terry