What is causing the difference in Bending moment between a case where there are no offsets and a case where the deck is offset to be at the top of the girder, when modeling a bridge superstructure?

Answer:

When the section offset feature is used, software basically creates a rigid link connecting the section centroid to the offset location.  Thus, a beam element would behave as if it has 2 rigid short columns at the end.  Kindly refer the description provided below in our online help manual.