Thanks for your thorough response.
For any thermal gradients affecting the bolted joints, I would say that their contribution for MoS calculations might be hand calculated for now. It seems to me that thermally induced forces affect the maximum and minimum preload in the fasteners, and that should depend only on the CTEs, Young's modulus and force ratio. Please correct me if I am wrong, and if I am missing something.
I do have another doubt, that perhaps needs to be addressed before the bolts analysis itself. How could I size the bolts correctly, i.e. how could I determine their workload and hence their diameter? I think I have read a post from you @peteroznewman in which you were saying to connect the parts with preliminary holes rigidly and then extract the forces? Could you please elaborate a bit about this?