We present an explainable AI-enhanced supervisory control framework for multi-agent robotics that combines (i) a timed-automata supervisor for safe, auditable mode switching, (ii) robust continuous control (Lyapunov-based controller for large-angle maneuver; sliding-mode controller (SMC) with boundary layers for precision and disturbance rejection), and (iii) an explainable predictor that maps mission context to gains and expected performance (energy, error). Monte Carlo-driven optimization provides the training data, enabling transparent real-time trade-offs. We validated the approach in two contrasting domains, spacecraft formation flying and autonomous underwater vehicles (AUVs). Despite different environments (gravity/actuator bias vs. hydrodynamic drag/currents), both share uncertain six degrees of freedom (6-DOF) rigid-body dynamics, relative motion, and tight tracking needs, making them representative of general robotic systems. In the space mission, the supervisory logic selects parameters that meet mission criteria. In AUV leader-follower tests, the same SMC structure maintains a fixed offset under stochastic currents with bounded steady error. In spacecraft validation, the SMC controller achieved submillimeter alignment with 21.7% lower tracking error and 81.4% lower energy consumption compared to Proportional-Derivative PD controller baselines. At the same time, in AUV tests, SMC maintained bounded errors under stochastic currents. These results highlight both the portability and the interpretability of the approach for safety-critical, resource-constrained multi-agent robotics.