Stop flattening config options added in config.php

[geordish]

Fixes #5454
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[mention-bot]

Thank you for submitting a PR @geordish! We have found the following @murrant, @laf and @paulgear based on the history of these files to review this PR.

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The inspection completed: No new issues

[Rosiak]

Doesn't seem to be breaking things on my dev install, so 👍