Those SPs you listed in regards to not having the "Is_MS_Shipped" flag should, in fact, NOT have the flag. They should not be marked as being shipped from Microsoft because they were not a part of the SQL 2005 distribution stored procedures.
Those SPs are actually created from Visual Studio; typically you will see them in SQL instances where VS was used to create a diagram. I'm sure there are other ways these procedures could become installed on a SQL instance.
Here is a link that specifically states that VS will create these Stored Procedures: http://msdn.microsoft.com/en-us/library/ms171974.aspx. You'll notice this list exactly matches your list.
I think in this instance we can see the value in being able to view a listing of stored procedures; in this case you were unaware that VS created these. Maybe there are more stored procedures you are not aware of that have been created?
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