Fix Legacy configuration not removed or updated

[jason810496]

closes: #46517

The inversed_deprecated_options logic in config_command.py causes config lint to retrieve the new section-option pair from the old section-option pair. Adding the lookup_from_deprecated_options argument can resolve the error.

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[jason810496]

Followup:

Should we add a pre-commit check to ensure the default configuration doesn’t raise issues with airflow config lint?
cc @Lee-W

[Lee-W]

Followup:

Should we add a pre-commit check to ensure the default configuration doesn’t raise issues with airflow config lint? cc @Lee-W

sounds like a great idea!