The formation of nematic liquid crystal (LC) superstructures in cells with non-uniform photo-alignment at the confining substrates is studied experimentally and by simulations. An interference pattern of left- and right-handed circularly polarized light is used to define the alignment at both substrates separately, so that the alignment varies along the x-coordinate on one substrate and along the y-coordinate on the other substrate. The interplay between the complex surface alignment and the liquid crystalline soft matter leads to the formation of interesting 3D configurations. The periodic LC structures that are formed in the bulk of the cell are analyzed experimentally by polarizing optical microscopy (POM) for different applied voltages. In the region with strong photo-alignment at both substrates, a 2D LC polarization grating (PG) with a complex 3D director configuration is formed. Distinct periodic structures with different symmetry properties are observed in the regions with weak illumination at the top and/or bottom substrate. The director configuration in the different regions was successfully simulated with the help of finite element (FE) Q-tensor simulations. The agreement between the simulations and the experiments was verified by comparing the POM images with simulated results for the transmission between crossed polarizers.