There does not seem to be an easy way to override the layout of fields that are part of the component configuration, i.e. the options for the component via com_config.
Stepping through the code when the layout is processed the FileLayout.php (J4) gets the layout paths but the paths are relative to com_config, not the component you are setting the options for. (I have not stepped through the code for J3 but I suspect the process is the same).
It is possible to override the layout for a particular field by setting the layout= in the config.xml (again for J4), but, these layout overrides must be in the root layouts directory and I have not found a way to have them installed into that directory during component installation via the manifest xml file.
It would be possible to do so using a pre/post flight scripts to move them there but I am not sure this is the best/correct way to do it.
My reason for doing this is to handle the differences between J3 & J4 so I can use the same installation. J3 uses type radio in layouts/joomla/form/field/radio while J4 uses layouts/joomla/form/field/radiobasic or layouts/joomla/form/field/radio/switcher. My thought was to use an override file that checked the JVersion and include the correct one. I have run into this issue though.