I'll use an example: I often need to create "Warning Notes" (aka "Admonitions") in my documentation. Those notes need to stand out, but they also need to not break the flow of reading. I need them to be visible, but easy to spot with the eye and ignore. It makes reading the doc and ignoring less important information easier. With Markdown, I can't create those notes.
Other interesting and useful thing is the ability to use variables. This allows me to make the documentation dynamic. Imagine, for example, a documentation that has many CURL requests examples that must include an X-Auth-Token. I can dynamically generate the documentation with the Auth-Token of the user reading the doc, allowing them to Copy/Paste the examples without having to modify them first.