Cost allocation, optimization, and diagnosis are the main application fields of thermoeconomics. Cost allocation allows evaluating the plant cost formation process. For plants containing dissipative equipment, the use of total exergy flows in the conventional productive diagrams is not able to isolate these components. The physical exergy disaggregation, despite increases the complexity, allows the treatment of dissipative equipment and residues. Nevertheless, conventional productive diagrams based on productive flows and fictitious units to connect the subsystems, may not take into account the physical connections existing in the system flowsheet, making the cost formation process arbitrary. The comprehensive diagram uses both flow types, physical and productive, and the subsystems are interconnected according to the physical flows of the flowsheet. This work aims to demonstrate that the combination of exergy disaggregation and comprehensive diagram avoids arbitrariness. The application of the localized exergy disaggregation at the comprehensive diagram reduces the complexity. A gas turbine cogeneration system is chosen as one application example. Productive and comprehensive diagrams are compared with total and localized disaggregation and a systematic procedure to treat waste and dissipative equipment is presented. The reduction of complexity is performed by means of localized disaggregation and the arbitrariness related to the productive diagram is evaluated.