SetCommands write all commands (needed for failsafe commands). As the stab commands only contains roll, pitch, yaw and thrust and all other commands to zero, the SetCommands(stab_cmds) will erase previously set auto_rc commands.
If we assume the 4 standard commands are mandatory, we can make a specific macro to set them (like it was before). The other option is to directly fill the commands vector from stab control loops. Which one is the best do you think ?