Shigley's method uses only geometry, therefore the bolt hole location is constant so rigid materials better represent the method. Since Shigley uses only geometry, there is no weighting factor to account for different bolt diameters so making the bolts all equal better represents the method.
Shigley's method and the EN 1993:1-8 standard are useful for making design decisions, but an FEA model with the true material Young's modulus and the true bolt diameters creates forces that better represent reality.