The static structural model provides a pre-stress solution to the modal analysis to adjust the stiffness matrix to make add the stiffening that the loads provide, but don't apply the loads in the downstream response spectrum analysis, so there are no stresses in the beams that the preload would have created. It's just that the stiffness of the beam has been increased by the tension.
Therefore the results you obtained in the response spectrum are what I would expect. You can add the stress results from the static structural bolt pretension to the stress results from the response spectrum to get the total stress.
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