The physical interaction of the convecting asthenosphere and the highly viscous lower lithosphere determines the transmission of plate driving stresses from the mantle to the plates, and controls the stress state of deep cratonic roots, which is important for cratonic diamond formation models. A growing number of studies have highlighted a high degree of heterogeneity in root zones, however, little work has been done on how a heterogenous lower lithosphere affects plate-mantle coupling. The purpose of this work is to assess the degree that physical and rheological heterogeneity in the lowermost lithosphere affects the coupling and transmission of stress from the asthenosphere to the lithosphere. Southern Africa is an area where fine scale variations in the seismic and lithological structure have been identified. Here we present numerical models of the dynamics of stylised and Southern Africa-like cratonic roots in a convecting mantle. We find lithosphere structure exerts a strong control on asthenospheric flow and this dominates the lower lithosphere stress field. Weak metasomatic zones do not systematically affect the stress regime, though they do mitigate the effects of stress extremes on root zones. Short length-scale finger-like features as seen in Southern African tomography are not stable over geological time periods for plausible rheologies, which suggests such small-scale variations in the seismic structure may have a chemical/metasomatic origin. Such chemical heterogeneities can be remarkably long-lived (order of hundreds of Myrs), despite their lack of mechanical integrity.