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We report ab initio benchmark calculations of nuclear matrix elements (NMEs) for neutrinoless double-beta ($0νββ$) decays in light nuclei with mass number ranging from $A=6$ to $A=22$. We use the transition operator derived from light-Majorana neutrino exchange and evaluate the NME with three different methods: two variants of in-medium similarity renormalization group (IMSRG) and importance-truncated no-core shell model (IT-NCSM). The same two-plus-three-nucleon interaction from chiral effective field theory is employed, and both isospin-conserving ($ΔT=0$) and isospin-changing ($ΔT=2$) transitions are studied. We compare our resulting ground-state energies and NMEs to those of recent ab initio no-core shell model and coupled-cluster calculations, also with the same inputs. We show that the NMEs of $ΔT=0$ transitions are in good agreement among all calculations, at the level of 10%. For $ΔT=2$, relative deviations are more significant in some nuclei. The comparison with the exact IT-NCSM result allows us to analyze these cases in detail, and indicates the next steps towards improving the IMSRG-based approaches. The present study clearly demonstrates the power of consistent cross-checks that are made possible by ab initio methodology. This capability is crucial for providing meaningful many-body uncertainties in the NMEs for the $0νββ$ decays in heavier candidate nuclei, where quasi-exact benchmarks are not available.