I'm not sure I would use Word's design philosophy as a relevant data point here. If you want mapped CCs in your header/footer then just do it (Nike's design philosophy).
I'm not seeing the behaviour the OP described in the dotx file that was posted. If this is not reproducible on other machines then I would investigate whether there are any macros running on that machine (perhaps try starting in safe mode and see if the problem still persists). The mention of the problem being with the last CC in the story makes me think perhaps you need to exit the CC (which writes to the xml field) before leaving the footer.
You might also want to verify that the CCs are mapped to the same xml field with a macro like this.
Code:
Sub AuditCCs()
Dim aCC As ContentControl, aStory As Range
For Each aStory In ActiveDocument.StoryRanges
For Each aCC In aStory.ContentControls
Debug.Print aCC.Title, aCC.Tag, aCC.Range.Text
If aCC.XMLMapping.IsMapped Then
Debug.Print "", "", aCC.XMLMapping.XPath
End If
Next aCC
Next aStory
End Sub