Maybe I'm nut fully understanding the problem. I think it is the same problem I had in NWC1, and was glad to see the workaround in NWC2. Paste the following into two staves and layer them, and see if this is what you want.
!NoteWorthyComposerClip(2.0,Single)
|Clef|Type:Bass
|TimeSig|Signature:4/4
|Key|Signature:C
|Text|Text:"No Overrides - looks bad"|Font:StaffItalic|Pos:8
|Note|Dur:4th|Pos:2
|Note|Dur:4th|Pos:2
|Note|Dur:8th|Pos:2
|Note|Dur:8th|Pos:2
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=End
|Bar
|Note|Dur:4th|Pos:3
|Note|Dur:4th|Pos:3
|Note|Dur:8th|Pos:3
|Note|Dur:8th|Pos:3
|Note|Dur:8th|Pos:3|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:3|Opts:Stem=Down,Beam=End
|Bar
|Text|Text:"Extra note spacing"|Font:StaffItalic|Pos:8
|Note|Dur:4th|Pos:2|Opts:XNoteSpace=1
|Note|Dur:4th|Pos:2|Opts:XNoteSpace=1
|Note|Dur:8th|Pos:2|Opts:XNoteSpace=1
|Note|Dur:8th|Pos:2|Opts:XNoteSpace=1
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=First,XNoteSpace=1
|Note|Dur:8th|Pos:2|Opts:Stem=Down,Beam=End,XNoteSpace=1
|Bar
|Text|Text:"Extra Stem Length"|Font:StaffItalic|Pos:8
|Note|Dur:4th|Pos:3
|Note|Dur:4th|Pos:3
|Note|Dur:8th|Pos:3|Opts:StemLength=9
|Note|Dur:8th|Pos:3|Opts:StemLength=9
|Note|Dur:8th|Pos:3|Opts:Stem=Down,StemLength=9,Beam=First
|Note|Dur:8th|Pos:3|Opts:Stem=Down,StemLength=9,Beam=End
!NoteWorthyComposerClip-End
!NoteWorthyComposerClip(2.0,Single)
|Clef|Type:Bass
|TimeSig|Signature:4/4
|Key|Signature:C
|Note|Dur:4th|Pos:1
|Note|Dur:4th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=End
|Bar
|Note|Dur:4th|Pos:1
|Note|Dur:4th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=End
|Bar
|Text|Text:"Zero Stem Length"|Font:StaffItalic|Pos:-11
|Note|Dur:4th|Pos:1|Opts:StemLength=0
|Note|Dur:4th|Pos:1|Opts:StemLength=0
|Note|Dur:8th|Pos:1|Opts:StemLength=0
|Note|Dur:8th|Pos:1|Opts:StemLength=0
|Note|Dur:8th|Pos:1|Opts:Stem=Down,StemLength=0,Beam=First
|Note|Dur:8th|Pos:1|Opts:Stem=Down,StemLength=0,Beam=End
|Bar
|Note|Dur:4th|Pos:1
|Note|Dur:4th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=First
|Note|Dur:8th|Pos:1|Opts:Stem=Down,Beam=End
!NoteWorthyComposerClip-End