The header update would be a good start for moving to some sort of block reference system. Obsidian can already update links when a filename changes, headers shouldn’t be impossible. (edit: already planned )
I’d like to see transcluded header title visibility toggling added as well. e.g:
note.md >
# Header
Some text
should be able to be displayed as
some text
when transcluded rather than
# Header
Some text
as it is now.
A switch in settings to control it should be enough.