It's insivible but it's present, so NWC makes room for it. :)
!NoteWorthyComposerClip(2.75,Single)
|Chord|Dur:Half,Dotted|Pos:-3,b-1,n0,3|Opts:Stem=Up
!NoteWorthyComposerClip-End
!NoteWorthyComposerClip(2.75,Single)
|Chord|Dur:Half,Dotted|Pos:-4z,-3,b-1,n0,3|Opts:Stem=Up
!NoteWorthyComposerClip-End
By the way: what about a way, in edit mode, to "see" that something invisible is there?
If I didn't know what's going on I would have been very puzzled and I had to check attentively the nwctxt.
The notehead is blank, as opposed to hidden, which is an important distinction. If you want the chord to behave as though the note is not there, then removing it is the only way.
As for showing an indication in edit mode, this is certainly doable. No promises at this point...