This may currently be achieved by modifying userchrome.css (for Linux users, it should be under $HOME/.config/joplin-desktop/). For instance, to move a specific notebook to the very end of the list:
Toggle own sort order is about the sorting of notes within a notebook, not the notebooks themselves.
After enabling toggle own sort order on a notebook, you can use the sort button within the notebook to change the sort, and it should only impact notes within that notebook.: