The APU build configuration uses Standard S32DS toolchain for APU targets to support APEX2 image cognition processor.
The APU Disassembler, APU C Preprocessor and APU C++ Preprocessor tools are not used in the build system and designed to manually get disassembler/preprocessor output for the selected files.
To configure the tool settings, right-click the project in the Project Explorer view, choose Properties and go to the tab.