The savvier ones probably have a little more — latex, markdown and lout, but the tooling pretty much ends there with stripped down, dumbed out features like boldface and italics and rather weak formatting due to the requirement of reflow. By the way did you know that reflow is no longer necessary for ebooks?

There's some support for inline images too but the standards haven't progressed enough in the past 15 years. Even those images tend to float away with reflow leaving little for the book designers to hold on to. To sum it up existing ebook ecosystem is just as lifeless as the dead-tree one it intends (supposedly) to replace. Unlike web that has grown and is in abundance today, ebooks have remained stuck in the 90's for years.

Another difference between books and apps is that books are expected to have a rigid spine to hold the pages together. A spine that binds and restricts the content in a linear read order that behaves very much like its atomic counterpart. Some native ebook readers, like the Kindle & iBooks app provide this feature correctly but the web seems to be lagging.