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It`s expected that applying the displacements separately would give a lower value because they are assumed to be uncorrelated in the crude sort of way that is obtained with SRSS. If you did an algebraic sum combination you would get the SPRS value.
Imagine a long structure supported at two nodes at one end. If one of the nodes is displaced in the axial direction, the participation factor obtained will be based on the large rigid body rotation this excitation produces. If the nodal excitations are correlated, this rotation does not occur. In general, if the excitations are known to be fully-correlated, the first two methods are correct. If uncorrelated the third method is more appropriate.
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