fix: do not overwrite comet config when set in InterceptConfigsPreRunHandler (backport #16395)

[mergify]

This is an automatic backport of pull request #16395 done by Mergify.
Cherry-pick of 0bded0d has failed:

On branch mergify/bp/release/v0.47.x/pr-16395
Your branch is up to date with 'origin/release/v0.47.x'.

You are currently cherry-picking commit 0bded0d19.
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Unmerged paths:
  (use "git add <file>..." to mark resolution)
	both modified:   CHANGELOG.md
	both modified:   server/util.go

no changes added to commit (use "git add" and/or "git commit -a")

To fix up this pull request, you can check it out locally. See documentation: https://docs.github.com/en/github/collaborating-with-pull-requests/reviewing-changes-in-pull-requests/checking-out-pull-requests-locally

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