The increasing use of drones for safety-critical applications, particularly beyond visual lines of sight and over densely populated areas, necessitates safer and more reliable designs. To address this need, this paper introduces a novel methodology integrating Null Controllability with the Model-Based Safety Assessment (MBSA) framework AltaRica 3.0 to optimize propulsor configurations and system architectures. The main advancement of this method lies in the automation of reliability modeling and the integration of controllability assessment, eliminating restrictions on the types of propulsor configurations and system architectures that can be evaluated and significantly reducing the effort required for each design iteration. Through a hexarotor drone case study, the proposed method enabled a high number of design iterations, efficiently exploring various aspects of the design problem simultaneously, such as configuration, system architecture, and controllability hypothesis, which is not possible with state-of-the-art techniques. This approach demonstrated significant reliability improvements by implementing and optimizing redundancies, reducing the probability of loss of control by up to 99%. The case study also highlighted the increasing difficulty of enhancing reliability with each iteration and confirmed that it is unnecessary to consider more than two simultaneous failures for design optimization. A comparison of reliability figures with previous studies highlights the crucial role of system architecture in effectively enhancing drone design reliability. This work advances the field by providing an effective multidisciplinary modeling framework for drone design, enhancing reliability in safety-critical applications.