The level of automation and precision in aircraft assembly determines the effectiveness and quality of aircraft manufacturing. In contrast, the unstable localization accuracy resulting from the layout pattern of flexible track drilling robot has limited their further development and applications in domains with high machining accuracy requirements, such as aircraft assembly. This study begins by presenting the paradox between the need for high-precision drilling tasks during aircraft construction and the lack of accuracy of automated drilling equipment. The problem of self-precision loss due to flexible track drilling devices is examined in a new application scenario where the overall position and pose layout change with the location of the process station. Then, the characteristics of the weak rigidity of the transmission system of the flexible track drilling robot at the joint surface and the variation of the transmission axial load due to variations in the position and pose of the drilling process station are examined. In addition, an equivalent stiffness model is developed to predict the incremental error of the entire process station, and the incremental error conjecture due to the elastic deformation of the coupling surface of the transmission system is proposed as an optimization algorithm for global position accuracy compensation. Finally, the incremental error conjecture is discussed and validated by designing ablation test groups one by one and evaluating the effect of the precision compensation algorithm. Experimental results showed that the incremental error compensation method optimized 68.67 percent of the total error.