In the early phases of the design of safety-critical systems, we need the ability to analyze the safety of different design solutions, comparing how different functional allocations impact the overall reliability of the system. To achieve this goal, we can apply formal techniques ranging from model checking to model-based fault-tree analysis. Using the results of the verification and safety analysis, we can compare different solutions and provide the domain experts with information on the strengths and weaknesses of each solution. In this paper, we consider NASA's early designs and functional allocation hypotheses for the next air traffic control system for the United States. In particular, we consider how the allocation of separation assurance capabilities and the required communication between agents affects the safety of the overall system. Due to the high level of details, we need to abstract the domain while retaining all of the key properties of NASA's designs. We present the modeling approach and verification process that we adopted. Finally, we discuss the results of the analysis when comparing different configurations including both new, self-separating and traditional, ground-separated aircraft.