Implement consistent model merging across the codebase

Context

In PR #795, we implemented smarter field merging for the nsys configuration by using exclude_unset=True in the model_dump() call. This allows partial overrides of nsys fields in scenario configurations while preserving base values from test definitions.

A similar approach was previously used for reports. However, the current approach for most other fields is "all or nothing" - meaning everything should be set at one level or another.

Proposal

Implement a consistent model merging strategy across the codebase:

1. Consider creating a unified merge_models(tdef, tscenario) function or similar utility
2. Apply the smarter merge approach consistently for all relevant model fields
3. Ensure the merging hierarchy is clear and well-documented

This would provide a friendlier and more intuitive user experience when overriding configuration values.

References

• PR: https://github.com/NVIDIA/cloudai/pull/795
• Discussion: https://github.com/NVIDIA/cloudai/pull/795#discussion_r2788287706
• Requested by: @amaslenn
• Related discussion with: @podkidyshev, @juntaowww