We address the linear stability of the two-dimensional incompressible flow past a square cylinder immersed in the wake of an upstream splitter plate, which separates two streams of different velocities, UT (top) and UB (bottom), to three-dimensional perturbations. The analysis is done in the so-called wake transition regime, across which two-dimensional vortex shedding incorporates spanwise modulation. In addition to the top and bottom stream Reynolds numbers (ReT,B=DUT,B/ν, with D the square cylinder side and ν the kinematic viscosity of the fluid), a parametric analysis is conducted to gauge the effects of splitter plate length (S) and the gap between the trailing edge of the splitter plate and the front face of the cylinder (G) on the leading three-dimensionalizing instabilities. Modes akin to the A- and B-type instabilities that characterize the wake transition regime past circular and square cylinders in homogeneous incoming flow are observed only at very small values of the top-to-bottom Reynolds number ratio R=ReT/ReB, while a third mode, mode C, is ubiquitous beyond more than very mild values of R. Increasing S at constant small G has a stabilizing effect on mode C, whose onset is pushed to higher values of R. Only for long S is mode A observed. Fixing a short S and increasing G results instead in a destabilization of mode C, and mode B is favored over mode A.