Inhomogeneous rough surfaces in which strips of roughness alternate with smooth-wall strips are known to generate large-scale secondary motions. Those secondary motions are strongest if the strip width is of the order of the half-channel height and they generate a spatial wall shear stress distribution whose mean value can significantly exceed the area-averaged mean value of a homogeneously smooth and rough surface. In the present paper it is shown that a parametric forcing approach (Busse & Sandham, J. Fluid Mech., vol. 712, 2012, pp. 169–202; Forooghi et al., Intl J. Heat Fluid Flow, vol. 71, 2018, pp. 200–209), calibrated with data from turbulent channel flows over homogeneous roughness, can capture the topological features of the secondary motion over protruding and recessed roughness strips (Stroh et al., J. Fluid Mech., vol. 885, 2020, R5). However, the results suggest that the parametric forcing approach roughness model induces a slightly larger wall offset when applied to the present heterogeneous rough-wall conditions. Contrary to roughness-resolving simulations, where a significantly higher resolution is required to capture roughness geometry, the parametric forcing approach can be applied with usual smooth-wall direct numerical simulation resolution resulting in less computationally expensive simulations for the study of localized roughness effects. Such roughness model simulations are employed to systematically investigate the effect of the relative roughness protrusion on the physical mechanism of secondary flow formation and the related drag increase. It is found that strong secondary motions present over spanwise heterogeneous roughness with geometrical height difference generally lead to a drag increase. However, the physical mechanism guiding the secondary flow formation, and the resulting secondary flow topology, is different for protruding roughness strips and recessed roughness strips separated by protruding smooth surface strips.