It is very kludgy and cumbersome to split project into several PCB (for example, stack of PCBs connected by backplane or headers, like Arduino & Shield for it) and/or to have variations of the PCBs for one schematics, like TH and SMD variants of the PCB for exactly same schematics.
Even in my very modest almost-electrical (as opposed to electronic) projects I need one or another from time to time.
As far as I understand it is limitation which is not easy to fix, because all architecture of KiCAD is based on this 1-1-1 principle.