Remove consensus internal options from cli flags

[jasagredo]

Description

Some of the options presented as cli flags seem to be consensus internal or low-level options. This PR adds warnings when they are set via cli flags in preparation for future removal, they can still be configured in the JSON/YAML configuration.

Checklist

• Commit sequence broadly makes sense and commits have useful messages
• New tests are added if needed and existing tests are updated. These may include:
  • golden tests
  • property tests
  • roundtrip tests
  • integration tests
    See Runnings tests for more details
• Any changes are noted in the CHANGELOG.md for affected package
• The version bounds in .cabal files are updated
• CI passes. See note on CI. The following CI checks are required:
  • Code is linted with hlint. See .github/workflows/check-hlint.yml to get the hlint version
  • Code is formatted with stylish-haskell. See .github/workflows/stylish-haskell.yml to get the stylish-haskell version
  • Code builds on Linux, MacOS and Windows for ghc-8.10.7 and ghc-9.2.7
• Self-reviewed the diff

[mgmeier]

For Performance & Tracing: we do make use of the snapshot options only via the --config file. We don't require them as CLI options.

[Jimbo4350]

LGTM! Updating the parser help with the configuration value needed to set in the config file would be useful.