Are you able to change your theme and see if that works? Either you don't have permission or the theme is hiding the menu. If you are able to add a Custom certificate to the course then you should be able to edit it, so my guess is the theme is hiding it. You could always search the DOM for 'Custom certification administration' and see if it is present in the HTML but is being hidden for some reason. The link to load the template is in the same menu as a whole bunch of other Moodle settings, see Chintan's screenshot below.
Custom certificate (plugin)
Custom Certificate in Adaptable
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