The Project Dependencies was already correctly set up. The bootloader project is already built before the application project. The problem is that the bootloader binary file is not created before compilation of the application project, so the application project build fails.
Stating it again: Project Dependencies is correctly configured, the problem is that the second project starts building before the bootloader binary is created.
Our workaround for the past few months has been to manually build each project in order. This allows the bootloader binary to exist at the time of the main application compile.