peteroznewman
Subscriber

Use at least 2 beam elements so you can easily apply bolt preload. You don't need more elements for accuracy.
A Fixed Joint has only one coordinate system, the joint coordinate system. If that csys is near one surface and far from the other surface, the rigid elements to the far surface become very long while the rigid elements to the near surface are very short. When the behavior of the Fixed Joint is set to Deformable, the length of the rigid elements is used in the distribution of forces to the nodes, so the distribution gets distorted by the different lengths. If the behavior of the Fixed Joint is set to Rigid, this is no longer a concern, but the solver will still have huge moments in the Fixed Joint that make convergence more difficult.
A Beam Connection has two ends so each surface is near one of the ends. The rigid elements from the center of the hole to the scoped surface are short and equal at both ends so the distribution of forces to the nodes does not get distorted. Since the length of the rigid elements in a Beam Connection are small compared to a Fixed Joint, the moments remain small and the solver can converge more easily
That is why I said a Beam Connection is a better choice than a Fixed Joint when the two surfaces are far apart. If they are close together and the Joint csys is located at the midpoint between the two surfaces, then it doesn't matter so much.
Your question on how does the beam elasticity affect the overall model response depends on whether the connection between the parts in the model is only the beam with no frictional contact and no bolt pretension or there is frictional contact and bolt pretension. Because in reality there is a bolt with pretension and contact between the flanges.
A Static Structural analysis can have contact between the flanges and a bolt pretension load. In this case, the beam diameter equals the bolt diameter, since the beam is there to represent the bolt as a part of the bolted joint. In step 2, you can apply an axial load on one side and calculate the axial stiffness of the bolted joint. You can also apply a moment to one side and calculate the rotational stiffness of the bolted joint.
Some analyses, like Random Vibration, require a linear model, so you can't have contact between the flanges and bolt pretension. In that case, the only connection is the beam. Don't use the diameter of the bolt for the diameter of the beam. The beam is not there to represent the bolt, it is there to represent the bolted joint. The joint has an axial stiffness much higher than the axial stiffness of the bolt. The joint has a rotational stiffness much higher than the bending stiffness of the bolt. You need to calculate the bolted joint axial and rotational stiffness in a nonlinear Static Structural model with contact and bolt preload, then calculate the beam diameter that creates the equivalent stiffness for the linear model.