Sigil is about EPUB
not the Kindle or the Ipad's warped versions.
Files do not define 'chapters' (although many of us put a chapter/section per file for ease of maitainence, that does not make it a 'chapter').
Sigil (not EPUB) used H tags as markers
to the auto-generator to define hierarchical TOC Levels (that most folk think of as Book/Part/Chapter) that are then coded into the NCX file. (
you can hand code the NCX and never use a H tag ).
Take some time and reverse engineer (with Sigil) some of the EPUBS found in the MR Library and figure out how things work for each book that you like the styling.