Insects have evolved over hundreds of millions of years to achieve exceptional agility, energy efficiency, and manoeuvrability. A key factor in their control capabilities is the use of efference copy mechanisms, which enable fast, robust control while maintaining sensors within their optimal operating range. Previous work has demonstrated the advantages of the efference copy-based fully-separable degrees of freedom (FSDoF) control architecture in single-input-single-output systems. However, insect flight control must handle multiple different time delays within distinct sensory and motor pathways. This paper presents a framework for designing FSDoF controllers, that phenomenologically model efference copies, for multi-input-multi-output (MIMO) systems with multiple different time delays (MDTDs). We provide a structured method for implementing FSDoF control on MDTD systems and benchmark its performance against model predictive control (MPC). Our results show that FSDoF achieves shorter settling times, smoother state transitions, lower actuation costs, and lower cross-coupling errors across a range of tested dynamics. Our findings highlight the potential of FSDoF control for biological and bio-inspired systems that operate under multiple different time-delayed dynamics.