[Bug] warn_error_options.silence not working within dbt_project.yml

[dbeatty10]

Is this a new bug in dbt-core?

• I believe this is a new bug in dbt-core
• I have searched the existing issues, and I could not find an existing issue for this bug

Current Behavior

CLI flag works:

dbt --warn-error-options '{"error": "all", "silence": ["TestsConfigDeprecation"]}' test --no-partial-parse

Environment variable works:

export DBT_WARN_ERROR_OPTIONS='{"error": "all", "silence": ["TestsConfigDeprecation"]}'
dbt test --no-partial-parse

But project flag in dbt_project.yml is not working for me no matter what I try:

flags:
  warn_error_options: {"error": "all", "silence": ["TestsConfigDeprecation"]}

flags:
  warn_error_options:
    error: all
    silence:
      - TestsConfigDeprecation

dbt test --no-partial-parse

Expected Behavior

I was expecting that the code example here would work to silence the warning. Instead, I get this:

[WARNING]: Deprecated functionality
The `tests` config has been renamed to `data_tests`. Please see
https://docs.getdbt.com/docs/build/data-tests#new-data_tests-syntax for more
information.

Steps To Reproduce

Create these files:

seeds/my_seed.csv

id
1

seeds/_seeds.yml

seeds:
  - name: my_seed
    columns:
      - name: id
        tests:
          - not_null

dbt_project.yml

# Seems to ignore the "silence" configuration (but still recognizes the "error" configuration):
flags:
  warn_error_options: {"error": "all", "silence": ["TestsConfigDeprecation"]}

Run these commands:

dbt seed

This raises an error presumably because the flags.warn_error_options.silence in dbt_project.yml it not taking effect:

dbt test --no-partial-parse

But silence works if using the CLI instead:

dbt test --no-partial-parse --warn-error-options '{"error": "all", "silence": ["TestsConfigDeprecation"]}'

Relevant log output

Compilation Error
  [WARNING]: Deprecated functionality
  The `tests` config has been renamed to `data_tests`. Please see
  https://docs.getdbt.com/docs/build/data-tests#new-data_tests-syntax for more
  information.

Environment

- OS:
- Python:
- dbt:

Which database adapter are you using with dbt?

No response

Additional Context

Originally discovered here: #10274 (comment)

[graciegoheen]

Closing as a dupe of #10160