--[BUGFIX] - Properly set instance user config from base passed base config.

[jturner65]

Motivation and Context

This PR properly copies the user defined attributes from a base config to an instance config's user-defined subconfig, instead of in the subconfig's base level.

How Has This Been Tested

Local c++ and python tests

Types of changes

• [ ] Docs change / refactoring / dependency upgrade
• [x] Bug fix (non-breaking change which fixes an issue)
• [ ] New feature (non-breaking change which adds functionality)
• [ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist

• [x] My code follows the code style of this project.
• [ ] My change requires a change to the documentation.
• [ ] I have updated the documentation accordingly.
• [x] I have read the CONTRIBUTING document.
• [x] I have completed my CLA (see CONTRIBUTING)
• [ ] I have added tests to cover my changes.
• [x] All new and existing tests passed.