NA28 Apparatus does indeed include the content that was previously included in the NA28 Crossrefs modules.
UBS5 Crossrefs should also be merged into UBS5 Apparatus. I will make a note to do so. We have gotten smarter at how we process files and it makes more sense to reduce the number of modules (especially with the limitations of mobile and parallel content).
GNT Notes is entirely separate. Rex Koivisto compiled this, and it is not associated at all with the official UBS or NA editions. It's safe to delete or stop using this.
I hope this helps to clarify.
(and I'm working on finishing the update with Appendix III as I type)