So if i'm understanding this correctly, it is more effective to use the denser fuels, because you are reducing the amount of "non propellant" mass(i.e. tank mass) added to the craft?
I took a tank and emptied the amount of Methane/Ox to match the amount of Hydrogen/Ox and the Methane/Ox tank got similiar dV(a small difference due to not having perfect control over fuel amount); however, i notice that it seems a "waste" to use the hydrogen since it takes up the same amount of "craft" space(the same size tank) when the Methane tank is damn near empty.
If this is the case, i still am confused about usage case for fuel types. Since endgame, we are not limited by the size of our craft, you should always use the most dense fuel, since this decreases your Tank:Fuel mass ratio, therefore utilizing the most Propellant Mass you can in that stage.