So the good news is that Help 3 has a rich API. If the Microsoft solution does not suit you then you can always use a 3rd party rich win32 or .NET solution. Or roll your own.
H3Viewer is something I quickly knocked together and shows a full TOC and full Index. Microsoft also allow you to make any browser or 3rd party viewer and make it the main viewer for VS 2010 (This was announced by Charles at a public conference but they
haven't made the mechanism public yet).