We characterize twisted right-angled Artin groups (T-RAAGs) that are subgroup separable using only their defining mixed graphs: such a group is subgroup separable if and only if the underlying simplicial graph contains neither induced paths nor squares on four vertices. This generalizes the results of Metaftsis-Raptis on classical right-angled Artin groups. Additionally, we show that the subgroup membership problem is decidable when the group is coherent, which occurs precisely when the defining mixed graph is chordal. We also address the rational and submonoid membership problems by exhibiting a cone-family of graphs for which the corresponding T-RAAGs have decidable rational and submonoid membership problems.