Fix: `clap` arguments are always overriding configuration

[dlachaume]

Content

This PR includes a fix that prevents clap arguments from systematically overriding the configuration with boolean arguments.

Pre-submit checklist

• Branch
  • [ ] Tests are provided (if possible)
  • [x] Crates versions are updated (if relevant)
  • [ ] CHANGELOG file is updated (if relevant)
  • [x] Commit sequence broadly makes sense
  • [x] Key commits have useful messages
• PR
  • [ ] No clippy warnings in the CI
  • [x] Self-reviewed the diff
  • [x] Useful pull request description
  • [x] Reviewer requested
• Documentation
  • [ ] Update README file (if relevant)
  • [ ] Update documentation website (if relevant)
  • [ ] Add dev blog post (if relevant)

Issue(s)

Relates to #1980

[github-actions[bot]]

Test Results

    4 files  ±0     55 suites  ±0   10m 46s :stopwatch: +20s 1 379 tests ±0  1 379 :white_check_mark: ±0  0 :zzz: ±0  0 :x: ±0  1 593 runs  ±0  1 593 :white_check_mark: ±0  0 :zzz: ±0  0 :x: ±0 

Results for commit 8a6fb72a. ± Comparison against base commit ef8c283f.