I’ve since found that the SCCM administrator has approved updates that supersede the patch that enables Enterprise Mode. Consequently IE 11 has been distributed without the Enterprise Mode patch.
Therefore a better way to deploy IE 11 with SCCM 2007 is to do so with a Task Sequence that deploys IE 11, then reboots, then deploys the IE 11 Enterprise Mode patch (KB3003057) and reboots again.