DockShelf is compatible with 10.11 and no new bugs have been found.
There is however a new feature which allows you to hide the menu bar and interferes DockShelf. When the menubar hides this signals DockShelf that the system has gone into full screen modes and automatically hides.
The end result of this means if you use menu bar hiding DockShelf will be hidden as well and not very usable. For now you’ll probably have to not use menu hiding along with DockShelf but a workaround for this is currently being worked on.