Remove flatten to improve deserialization error messages

[dhruvmanila]

Summary

Closes: #9719

Test Plan

Before:

ruff failed
  Cause: Failed to parse /Users/dhruv/playground/ruff/pyproject.toml
  Cause: TOML parse error at line 22, column 1
   |
22 | [tool.ruff.lint]
   | ^^^^^^^^^^^^^^^^
invalid type: string "false", expected a boolean

After:

ruff failed
  Cause: Failed to parse /Users/dhruv/playground/ruff/pyproject.toml
  Cause: TOML parse error at line 27, column 20
   |
27 | mypy-init-return = "false"
   |                    ^^^^^^^
invalid type: string "false", expected a boolean

[github-actions]

ruff-ecosystem results

Linter (stable)

✅ ecosystem check detected no linter changes.

Linter (preview)

✅ ecosystem check detected no linter changes.

[charliermarsh]

Great, thanks!