Hi,
I was referring to this link:
https://github.com/IDPF/epubcheck/issues/305
This issue is under review and of the last release of epubcheck 4 alpha having a DOCTYPE on a fallback ncx was considered acceptable. It seems someone disagrees with that on Apr 7, but I see no commit message or review to change epubcheck 4.
So this one may get reversed yet again. In epubcheck 3 it was okay, in epubcheck 3.1 it was an error, and in epubcheck 4 alpha it was no longer an error. So I guess this is a wait and see.
Either way KindleUnpack will keep the DOCTYPE on the ncx until epubcheck 4 final comes out and declares it one way or the other.