In Sigil the nav.xhtml is only movable in the Book Browser but that doesn't change where it's displayed when you look at the book in an e-reader; it's still at the end of the book. There is no secondary TOC. Here's what Calibre Editor's File Browser looks like after dragging the nav.xhtml to the top:
I'm also wondering why a secondary TOC is needed since the nav.xhtml file functions as one, after it's moved to the top in Calibre. The epub 3.2 spec says
"But the EPUB Navigation Document is not exclusively for machine processing. Because it is an XHTML Content Document, it can be part of the linear reading order, avoiding the need for duplicate tables of contents. Content which is only destined for machine processing, such as page lists, can be hidden from visual rendering with the hidden attribute."
https://www.w3.org/publishing/epub3/epub-packages.html