This work proposes a framework that generates and optimally selects task-specific assembly configurations for a large group of homogeneous modular aerial systems, explicitly enforcing bounds on inter-module downwash. Prior work largely focuses on planar layouts and often ignores aerodynamic interference. In contrast, firstly we enumerate non-isomorphic connection topologies at scale; secondly, we solve a nonlinear program to check feasibility and select the configuration that minimizes control input subject to actuation limits and downwash constraints. We evaluate the framework in physics-based simulation and demonstrate it in real-world experiments.