There seems to be a bug with MDSModelDeploy with the "deploynew" option: the MUID (the internal model ID in mdm.tblModel) from the source, which is stored in the package file when you create it, is not copied into the destinations mdm.tblModel when you use "deploynew". Instead, a new MUID is created, but the model name stays the same. This means you won't be able to later use MDSModelDeploy with the "deployupdate" option since the MUID's don't match. This bug does not happen if you use the model deployment wizard (it will use the same MUID from the source in the destination).
Note also that http://msdn.microsoft.com/en-us/library/ff486971.aspx is in error in saying the model deployment wizard will also copy the master data ("Master data is populated" under "Notes"), but it will not.
Also, on http://msdn.microsoft.com/en-us/library/hh479646.aspx and http://msdn.microsoft.com/en-us/library/hh479639 and http://msdn.microsoft.com/en-us/library/ff487019 and http://msdn.microsoft.com/en-us/library/ff486971.aspx, the spots where it says "model objects only" should really say "model objects/business rules/subscription views only", as the model deployment wizard deploys all three, not just model objects.