Answer to my question:
The capabilities displayed on the plugin management page are pulled from the user that’s managing the settings. WordPress doesn’t really have any place in which it stores a comprehensive list of capabilities (partially because some capabilities could potentially be added for a single user on a single page, so there would be no reliable way to catalog them all). Therefore, in order to gather the list of capabilities, this plugin simply retrieves the list of capabilities that the current user has.
If you are simply a Super Admin, without any role on the root site, you will only see the network capabilities; as WordPress doesn’t explicitly assign any capabilities to the Super Admin user. However, if you make yourself an Administrator on the root site, you should see quite a few more capabilities appear on the plugin management page.
Quoted from https://plugins.ten-321.com/extended-super-admins/#comment-3753
