Gary,
this option is useful if you have done a bare-metal deploy/restore to the client using the Ghost Boot Partition (GBP). Once Windows is installed on a client, generally it is not necessary to keep the GBP around since a virtual partition can be created as needed.
Keeping the Ghost Boot Partition might be useful in if the virtual partition doesn't work correctly or if you want to have files in the DOS partition persist between DOS operations, but usually overwriting the GBP is the right choice. If you are not actually using a GBP then this option does nothing.
Anakin