The valves used in the SM head are SM valves. The valves used in the Mopar head are stock Mopar valves. The valves used in the TF head are TF valves. The point of this was to show people using an all stock head what they can expect.
Your observation is correct. Valve length and installed height (relative to the shaft) do affect the geometry.
Edit: The rocker shaft saddle in the TF head has been relocated (by TF) to improve geometry.