It was a fantastic episode of Doctor Who. The storyline was amazing.
My guess would be that the burning of the body at the end of each loop cycle in the episode makes the skull indistinguishable from that of an old one.
There was simply too much trauma to the body/skull.
In answer to how often the doctor dies, I would guess that each loop cycle takes days/...
Utopia's End of the Universe would be older
in Listen we see where Orson's ship is
however in Utopia we see what Earth is like
the difference is indicated by The Doctor in Utopia
MARTHA: Is that a city?
DOCTOR: A city or a hive, or a nest, or a conglomeration. Like it was grown. But look, there. That's like pathways,...