But nobody wants the ToC inside an ePub. ePub has a perfectly good external ToC. Blame the conversion software for putting the ToC (from toc.ncx) at the back. That is a software conversion issue, not an issue with toc.ncx.
Why not log it as a bug in Calibre or make it a feature request to be able to specify where the ToC goes when converted from toc.ncx?