Collections cloned and indexes built before the admin.system.version collection will default to the lower FCV behavior because it will not have been initialized yet. See
SERVER-48054 for a concrete example of how this introduces a bug.
This has the potential to further introduce problems. Collection and index formats have the potential to be based on the FCV. We want to be able to assume our data is in a particular format if the FCV is set to a specific version, and at the moment that is not possible.
To be safe and to avoid future bugs, we should clone this collection first.