ChangeSummary is defined as a diff between the state of the graph when beginLogging was called, and the state when endLogging was called. The API used to modify the graph does not enter into the the definition.
Users that call DataObject.delete expect for the object to be represented in the change summary as a deleted object. Usually, that is what they get. But the description of the delete method seems to suggest that delete is rather more intended for implementing a pool of DataObjects, that are freed and later re-used in the graph. If delete is used in this way, it is possible that the "deleted" object appears as a modified object in the change summary.
The utility of implementing object pools is questionable to say the least. It seems more reasonable to say that the delete method is intended to indicate the object should be deleted...as opposed to detach, which is a step towards moving the object.