Backport REPO-785: Versioning operations via the VersionManager must be done with virtual layers disabled

This is already the case for the deprecated versioning operations on the node (such as node.checkin, node.merge, etc.) but needs to be implemented for the operations via the VersionManager interface as well. I ran into an overflowing stack because I was using the "new" methods.
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Check the possibility of backporting REPO-785 to 7.8