If you're using a 2 or 4 bolt unstiffened flush end plate, pg 37 of AISC design guide 39 says "In the design of bolts for shear forces, it is commonly assumed that all the shear force is resisted by the bolts at the compression flange. This is a convenient assumption that allows the tension and shear forces to be separated to different groups of bolts. Because the bolt tension produced by the moment is coupled with a compensating compression force on the other side of the axis of bending, the net clamping force does not reduce with applied moment, and the equivalent bolt pretension force from all bolts is active in resisting the shear force due to friction, although this resistance is not considered in design. However, if the connection is subjected to axial tension, it may be necessary to design the bolts for the combined effects of shear and tension."

TLDR: RISA likely takes the conservative approach of only considering the (2) bolts at the compression flange for shear.