This is already possible using Booktype themes and the normal HTML hierarchy of headings from H1 through to H6. For example, you may wish to have a page break before every H2 heading, representing a subchapter, which is possible using theme CSS.
By default, every chapter is expected to start with a H1 element. You may also wish to show H2 elements in the Table of Contents or PDF bookmarks, which you can do by modifying the mPDF output scripts.
Hmm, this sounds very complicated. Will these topics be covered in the Booktype manual? And in a way that may be understandable for "ordinary" people who does not know much about how to modify scripts?
I was hoping it could be possible to just "mouse drag" a chapter in the user interface to make it a subchapter of another chapter.
It's not likely that standard Booktype will implement sub-chapters in the editor's Table of Contents because this would change a lot of behaviours in the editor.