The vertical combinations requirements are intended for the case where one lateral force resisting system is used for an upper portion of a structure, and a second (or third) is used for the lower level(s). As an example, consider a three-story light wood (or CFS) frame structure mounted on top of a concrete or masonry (lower structure) that serves as a garage. The primary concern here is assuring that the lower structure has adequate strength to support the upper structure, considering its potential overstrength, and also that the lower structure doesn't yield prematurely (relative to the upper structure) and develop an inelastic weak/soft story. Of course this is all done in an approximate manner rather than thorugh explicit nonlinear anlaysis.
The horizontal combinations rules are intended for the case where different structural systems are used within the same story in the same direction of resistance. For example, consider a single story structure, with rigid diaphragm that has a concrete shear wall on one side and a steel braced frame on the other. The intent here is to account for deformation cocmpatibilty of the two systems considering their relative rigidities, and avoidance of development of inelastic torsional response.