Update the flag & environment table callouts

[ADubhlaoich]

Proposed changes

This pull request changes the warning callout about prefix changes to be more prominent and precise, and adjusts the formatting of the config-dirs note for readability.

Checklist

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• I have read the CONTRIBUTING document
• I have run make install-tools and have attached any dependency changes to this pull request
• If applicable, I have added tests that prove my fix is effective or that my feature works
• If applicable, I have checked that any relevant tests pass after adding my changes
• If applicable, I have updated any relevant documentation (README.md)
• If applicable, I have tested my cross-platform changes on Ubuntu 22, Redhat 8, SUSE 15 and FreeBSD 13

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