The mod/assign/settings.php need to be reworked:
1/ nothing module related can appear on the new install page
2/ mod_assign should not pollute global $CFG

Ideally settings should affect only one plugin, once you start adding dependencies things start to break. In this particular case we need to apply default settings in manual install and cli upgrades, the mod_assign gets executed before the subplugins, it can not depend on its settings being set. I do not know any elegant solution here, maybe show all plugins in assign_feedback_plugin_for_gradebook and default to so known plugin.

The second problem is that we can not keep adding module specific stuff to $CFG, long ago it was agreed that all new stuff goes config_plugins. Solution is to use:

admin_setting_configselect('assign/feedback_plugin_for_gradebook')

and the same for new admin_setting_configcheckbox('assignsubmission_' . $type . '_default', and otehr settings.