If you have installed Windows 7 or Server 2008 R2 through either the Windows media or MDT then you have noticed that a 100 – 300 MB system partition is created that is hidden when you finish in the final operating system (well it is not really hidden, it just doesn’t have a drive letter).  The Microsoft Windows team made that decision so that bitlocker could easily be enabled at a later time without having to repartition the disks.  However if you don’t ever plan on enabling Bitlocker on your Windows 7 or Server 2008 R2 systems you can use MDT with an extra variable in the customsettings.ini and MDT won’t create the extra partition.  The variable is:

DoNotCreateExtraPartition = YES