chore: improve pyproject.toml readability

[ajbozarth]

Misc PR

Type of PR

• Bug Fix
• New Feature
• Documentation
• Other

Description

• Link to Issue: Clean up and streamline pyproject.toml #453

Improves the readability and maintainability of pyproject.toml without changing functionality.

Changes

• Added section dividers using the repo's established style (matching tooling/ pattern)
• Consolidated MyPy configuration (moved overrides adjacent to main config)
• Cleaned up unused Ruff lint rule comments (removed B, PTH, RET, SIM, D107, UP006/007/035)
• Aligned inline comments consistently for better maintainability

Related Issues

Closes #585 (invalid - Ruff recommends pyproject.toml)
Closes #586 (invalid - Pytest doesn't support pytest.toml)

Part of #453 (streamline pyproject.toml)

Testing

• ✅ ruff check pyproject.toml passes
• ✅ Pre-commit hooks pass
• ✅ No functional changes to tool configurations

Testing

• Tests added to the respective file if code was changed
• New code has 100% coverage if code as added
• Ensure existing tests and github automation passes (a maintainer will kick off the github automation when the rest of the PR is populated)

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