It's impossible.
From teh ebgining of the game you'll get a Dragon Stone and the Crystal Skull without any exceptions.
I think I may be misunderstanding you, or you may be mistaken.
The only item you have "from the beginning of the game", assuming you are using no cheats/trainers, or DLCs, is a single book. DLCs add only armour and weaponry. But perhaps by "the beginning of the game", you mean "Broken Valley", in which case, yeah, I totally agree.
The crystal skull is found on some monsters (called "Creatures" in the English version), which are in a mine - if I remember right, the mine's off to the far west of Broken Valley.
