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This paper presents an approach to multidisciplinary optimization (MDO) of transport aircraft that attempts to strike a balance between two broad classes of MDO approaches: those arising from the formal optimization background, and those coming from the aircraft design background. It starts from the observation that any kind of numerical design process can be viewed as an approximation of a formal optimization process, where Jacobians of cost functions may be inexact and are often not explicitly computed. Based on that, a specific MDO problem representation and a highly parallel process assembly and execution protocol (the "cybermatrix" protocol) is defined, as well as one possible realization on high-performance computing (HPC) resources. The approach is applied to an optimization of a long-range transport aircraft, employing disciplinary subprocesses for high-fidelity aerodynamic design