Yeah, we only use simple mode - it's advanced mode that everyone needs to watch out for - it doesn't do what you expect (it's optimized for combining multiple files, not producing one file).
If you carefully read the instructions, you can learn how to compile libraries with it - there is explicit support for this use case. (which is likely what jQuery have done.)
Actually it's not really efficient for us to do that - since we would need to expose literally everything and in the end we would end up with the same result as running it through the simple minifier. As it turns out though the simple minifier is quite good - giving us a 13% improvement over YUI Min.