The issue here I believe is a question of hierarchy, not really indents. (For the Kindle's Go To menu)
Hierarchical ToCs will be created with calibre's ToC generator, if using the appropriate header tags. Or manually editing the ToC of course.
If the EPUB has a hierarchical ToC, either kindlegen or calibre-convert will preserve it into AZW3, and the Go To menu on the Kindle will have a hierarchical ToC. After that it is up to the Kindle to interpret.
You will see exactly what you see with the User Guide from Amazon.
(NOTE: I believe I heard somewhere that a Kindle bug breaks collapsible/hierarchical ToC if the first element has children.)