SW4STM32 and SW4Linux fully supports the STM32MP1 asymmetric multicore Cortex/A7+M4 MPUs

   With System Workbench for Linux, Embedded Linux on the STM32MP1 family of MPUs from ST was never as simple to build and maintain, even for newcomers in the Linux world. And, if you install System Workbench for Linux in System Workbench for STM32 you can seamlessly develop and debug asymmetric applications running partly on Linux, partly on the Cortex-M4.
You can get more information from the ac6-tools website and download (registration required) various documents highlighting:

System Workbench for STM32

Run configuration for a CubeMX imported program

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.