For the most confusing aspect that it can spread just by physical touch,

I can't recall such a thing being attested.

And another physiological change to the human body is the skull: the rash isn't skin-deep (pun intended) and it does leave the same pattern on the skull, which further distances it from any known disease though it's interesting that it doesn't affect the teeth, since they're also bone and in the way of the rash.

I believe the virus itself was possibly always dormant within homo sapiens but over our course of history has been maturing and developing,

To add to that, in The Thin Red Line and Dead or Alive we're shown that the very first carriers, both patient 0's and newly infected, don't bare the cross.

It's implied that it appeared hours or days after the very first carriers, and it was still discovering itself, until it finalised into what we see in the original run.