feat: preserve unknown config keys in extensions

[extrasmall0]

Summary

• add an extensions field to ConfigurationLoader for downstream-owned config
• route unknown top-level keys from from_dict() into extensions instead of raising TypeError
• allow callers to merge explicit extensions with unknown top-level keys
• add coverage for passthrough, merge, and validation behavior

Testing

• uv run pytest tests/unit/setup/test_configuration_loader.py -q

Closes #1652