Ownership is a relationship between two top level windows while Parent is a relationship between a top level and a WS_CHILD, or a WS_CHILD and another WS_CHILD.
The parent of a button is the form it is on, while a message box is owned by the form that showed it.
Read this article from Microsoft Win32 Window Hierarchy and Styles to get a much clearer understanding of Ownership, Parenting, ZOrder, SetWindowLong, GetWindow and all the other nasty bits of the Win32 api for creating window relationships.
EDIT: Looks like Microsoft took down that content, here is another reasonable summary of Ownership / Parenting.