Is there any way to override the template files located in owncloud/settings/templates/... in a similar way to how theme files can be overridden in owncloud/custom/...? It’s not practical for me to edit the source files located in owncloud/settings/templates directly.
Unless I’m not understanding the docs correctly I cannot override / extend the templates located in the settings directory (eg owncloud/settings/templates/tokensendnotify.php) in the same way that I can override template files located in the owncloud/core/templates directory using a owncloud/custom directory.
There you can add the folders /settings/templates with the templates you want to override.
When you want to rename the theme, rename the folder and the id value in /appinfo/info.xml
(recommendation: only use theme-yourname w/o any other special characters as id/name.
Along with the documentation linked above you should have your theme working soon