Also noted an error in the Application log with the following content:
(PID 7684, Thread 3) Task Get-OwaVirtualDirectory writing error when processing record of index 0. Error: Microsoft.Exchange.Management.Metabase.IISGeneralCOMException: An IIS directory entry couldn't be created. The error message is Access is denied.
. HResult = -2147024891 ---> Microsoft.Exchange.Management.Metabase.COMDetailException: Access is denied.
One could assume this relates to a permission issue but the user running the rollup is an enterprise administrator so it must be something else related to security. Also note that I'm currently working with MS on this and posting updates here for other people with the same problem.