Your older custom shortcuts got added to the Shortcuts to line up with the new Settings scheme, that is why they still work and are there (i think i understood you correctly since you mentioned the file kglobalshortcutsrc). When installing the khotkeys you get back the Custom Shortcuts entry in Settings, but the list is not backwards compatible AFAIK, hence will not be displayed there. khotkeys is no longer a requirement and it even might get obsolete …
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