Thanks for the reply. I've done that with Genesis Plus GX which creates the system config files in the config folder. genesis,cfg, megadrive.cfg etc, but those config files don't have any of the core options that i wanted to save to them. They only contain shader, overlay, video settings.
If i manually copy, paste and adjust the core options i want from the retroarch-core-options.cfg to each of the content directory override files, nothing changes for those specific systems. Seems to always want to read from the retroarch-core-options.cfg file.