I hate to bump my post but… the issue is still there.
See for instance this post by @Nils: Note creation without highlight (sticky note/post-it note) - #6 by Nils. The note is added to page 152 (or 153) of the doc but MN3 shows page 170.
What I called “logical page numbering” in my original post is more precisely called “page labels” and is defined in the Document Catalog object of the PDF.