The immense growth in e-Commerce has intensified the need for efficient last-mile delivery systems. This paper introduces an enhanced Two-Echelon Vehicle Routing Problem with Drones (2E-VRPD) that addresses critical limitations by hyperparameter tuning using Bayesian optimization. A new algorithm is proposed that extends the original Drone Truck Route Construction (DTRC) algorithm by incorporating clustering for customer segmentation and Bayesian optimization using the OPTUNA framework for dynamic synchronization of trucks and drones. Experiments with benchmark instances and real-world case studies demonstrate an average reduction of 9.6% in delivery time.