Achieving low thermal conductivity and good electrical properties is a crucial condition for thermal energy harvesting materials. Nanostructuring offers a very powerful tool to address both requirements: in nanostructured materials, boundaries preferentially scatter phonons compared to electrons. The computational screening for low-thermal-conductivity nanostructures is typically limited to materials with simple crystal structures, such as silicon, because of the complexity arising from modeling branch-and wave vector-dependent nanoscale heat transport. The phonon meanfree-path (MFP) dependent Boltzmann transport equation (MFP-BTE) approach is a model that overcomes this limitation. To illustrate this, we analyze thermal transport in 75 nanoporous half-Heusler compounds for different pore sizes. Our calculations demonstrate that, in most cases, the optimization of thermal transport in nanostructures should take into account both bulk thermal properties and geometry-dependent size effects, two aspects that are typically engineered separately. To enable efficient calculations within this paradigm we derive a model, based on the "gray" formulation of the BTE, that can decouple the influence of the geometry and the material on the effective thermal conductivity with relatively little loss in accuracy compared to the MFP-BTE. Our study motivates the need for a holistic approach to engineering thermal transport and provides a method for high-throughput low-thermal conductivity materials discovery.