Motion control of flexible joint robots (FJR) is challenged by inherent flexibility and configuration-dependent variations in system dynamics. While disturbance observers (DOB) can enhance system robustness, their performance is often limited by the elasticity of the joints and the variations in system parameters, which leads to a conservative design of the DOB. This paper presents a novel frequency response function (FRF)-based optimization method aimed at improving DOB performance, even in the presence of flexibility and system variability. The proposed method maximizes control bandwidth and effectively suppresses vibrations, thus enhancing overall system performance. Closed-loop stability is rigorously proven using the Nyquist stability criterion. Experimental validation on a FJR demonstrates that the proposed approach significantly improves robustness and motion performance, even under conditions of joint flexibility and system variation.