This is expected behavior and functioning as designed. Shortcut Center is trying to edit the Shortcut with its original state being the actual setting used by the Shortcut. Clicking "Clear All Values" will result to the original state (which is the actual saved Shortcut).
For example, when creating a shortcut with Number of Copies set to 5, 5 is the default/original value. Therefore, when pressing the "Clear All Values", Number of Copies is still set to 5.
This is different from native Shortcuts where, when the user loads a Shortcut from the Native workflow, such as Copy/Email/FTP/Fax, the original state is the setting created by administrator. Thus, when clicking the "Clear All Values", it will revert to that original state.
For example, navigate to Default State > Invoke Copy Workflow > Load Shortcut, and by pressing the Star icon, the number of copies is changed from 1 to 5. However, this time, clicking on "Clear All Values" will set the Number of Copies to return to the value of 1.