The title seems to be somewhat misleading. What you’re correctly pointing out is the difference in procedure when you are applying contrib updates to a codebase as opposed to when somebody else made those changes (at which point there doesn’t need to be any difference between a deployment that does or does not contain contrib updates; run updates, import config). Your central point is that the update process may apply changes to the configuration. When one understands that, the rest makes perfect sense.
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The title seems to be somewhat misleading. What you’re correctly pointing out is the difference in procedure when you are applying contrib updates to a codebase as opposed to when somebody else made those changes (at which point there doesn’t need to be any difference between a deployment that does or does not contain contrib updates; run updates, import config). Your central point is that the update process may apply changes to the configuration. When one understands that, the rest makes perfect sense.