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This paper explores the design space for thermal management in electric vertical take-off and landing aircraft using model-based approaches. The aim is to develop and validate a model-based design optimization method for predicting real-time battery thermal behaviour. BTMS test rig configurations are employed to investigate the design of battery sub-packs and thermal systems, integrated with thermal modeling for simulation-based analysis. Additionally, parametric design optimization utilizing Genetic Algorithm (GA) and Simultaneous Perturbation Stochastic Approximation (SPSA) methods was implemented to enhance thermal distribution while reducing structural weight. At a 30% state of charge, performance metrics improve by 3.64% when employing a detailed thermal module battery compared to a lumped module, along with a 2.67% increase from the use of an edge module. The simulation decreased the average peak temperature by up to 22% when active cooling and logical thermal variant sweep strategies were applied. Results from simulated missions demonstrate effective thermal regulation, with temperature gradients maintained within safety thresholds. This approach enables the early-stage validation of battery thermal strategies within aviation design workflows. Mission-specific optimization establishes the foundation for integrating thermal modules in next-generation electric aircraft. These insights underscore the feasibility of the research idea for engineering implementations.