I have a CubeMX “Debug” program in my board and it will automatically start/run at power on. The debug symbols are not loaded into the board. If your program won’t start at power on, removing the symbols from the elf file is unlikely to fix the problem.
Any changes you make to add a new configuration will likely be lost if you regenerate the CubeMX project. If you just need to create a stripped elf, it may be easier to do it outside of Eclipse.