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Quantum state tomography (QST) represents an essential tool for the characterization, verification, and validation (QCVV) of quantum processors. Only for a few idealized scenarios, there are analytic results for the optimal measurement set for QST. E.g., in a setting of non-degenerate measurements, an optimal minimal set of measurement operators for QST has eigenbases which are mutually unbiased. However, in other set-ups, dependent on the rank of the projection operators and the size of the quantum system, the optimal choice of measurements for efficient QST needs to be numerically approximated. We have generalized this problem by introducing the framework of customized efficient QST. Here we extend customized QST and look for the optimal measurement set for QST in the case where some of the quantum gates applied in the measurement process are noisy. To achieve this, we use two distinct noise models: first, the depolarizing channel, and second, over- and under-rotation in single-qubit and to two-qubit gates (for further information, please see Methods). We demonstrate the benefit of using entangling gates for the efficient QST measurement schemes for two qubits at realistic noise levels, by comparing the fidelity of reconstruction of our optimized QST measurement set to the state-of-the-art scheme using only product bases.