If I recall correctly, if something is within the organic material it's transported - that's why the Terminators were covered in skin so they could transport back in the original movie.
Perhaps there was still enough skin covering the skull during transport that it could go.
I didn't really like that sequence, though, when the 1999 Terminator found all its parts in 2007. I could have thought of a cleverer way of bringing the threat forward.
I am
Dawg
I agree it could have been done much better and there are still things it seems they need to clean up. But it is worth watching and giving it a chance from my viewpoint, It is sci-fi and i support that because i want good sci fi on TV!