docs: clarify CLI usage

[erickzhao]

• I have read the contribution documentation for this project.
• I agree to follow the code of conduct that this project follows, as appropriate.
• The changes are appropriately documented (if applicable).
• The changes have sufficient test coverage (if applicable).
• The testsuite passes successfully on my local machine (if applicable).

Summarize your changes: A few formatting changes, as well as a note on dot notation for nested CLI flags.

[codecov]

Codecov Report

Merging #1534 (d29a94f) into main (6cdd96b) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##             main    #1534   +/-   ##
=======================================
  Coverage   95.58%   95.58%           
=======================================
  Files          15       15           
  Lines         793      793           
=======================================
  Hits          758      758           
  Misses         35       35           

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