--[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
• 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

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