You could duplicate the Building Material (BM) and its Cut Fill as well. The Column's BM should use the first Cut Fill, the Beam's BM should use the duplicate. Also, set the Intersection Priority Number of the Column's BM to a higher value than the Beam's BM. This way the Column will cut the Beam because of the higher Intersection Priority Number, and since they have different Cut Fills (although their patterns appear identical) the fills will not be merged in Section.
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