Ab initio Green-Kubo (aiGK) simulations of heat transport in solids allow for assessing lattice thermal conductivity in anharmonic or complex materials from first principles. In this work, we present a detailed account of their practical application and evaluation with an emphasis on noise reduction and finite-size corrections in semiconductors and insulators. To account for such corrections, we propose strategies in which all necessary numerical parameters are chosen based on the dynamical properties displayed during molecular dynamics simulations in order to minimize manual intervention. This paves the way for applying the aiGK method in semi-automated and high-throughput frameworks. The proposed strategies are presented and demonstrated for computing the lattice thermal conductivity at room temperature in the mildly anharmonic periclase MgO, and for the strongly anharmonic marshite CuI.