I am not sure what "calibre creates a metadata toc not a toc inside the document" means. When I look at this tutorial link, I get the impression it can create a table of contents similar to the output in mobipocket.
It even shows the output.
Pardon my ignorance then, but Calibre then doesn't create a table of contents one can see after the title page? and which when you tap on the chapter, it takes you to it.
http://amalthia.mediawood.net/tutorials/ebooks/toc.html
Thank you for taking the time to respond.