Bugfix: ConfigDict.user_values() should return only child entries, not instance itself

[mrmundt]

Fixes #3721

Summary/Motivation:

@shermanjasonaf reported an issue with ConfigDict.user_values(). This PR fixes that problem by introducing a new private flag and adds two tests that mimic the examples given in the Issue.

Changes proposed in this PR:

• When making a ConfigDict from a dict, only the entries are marked as user-set, not the instance itself
• Tests

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