As far as I know when you are flying VFR there is no clearence given to any altitude. I think what you are talking about applies only to the lessons. I know that some of the lessons will tell you that you need to be at a specified altitude when crosing a waypoint weather it is a VOR NDB or INTERSECTION. This applies to what is called controlled airspace. But in all of my VFR flights I make I have never had ATC tell me that I need to cross a point at a specific altitude..
  VFR flight means that you are responceable to clear yourself before you make any change in your flight path.

But in the real world there are controlled airspaces where in order to fly through you must be at a specified altitude or you can not fly through it