Why are the lines from the zone manifold to the zone headers made of copper and only change over to pex passed the zone header? Can pex be used starting at the zone manifold (using bigger diameter pex) and then once arrived at the zone change over to the smaller diameter pex loops using a T?

sure. You wont have a very professional look, wont be able to balance, have a look at the Sioux Chief copper manifolds, they are not to expensive, will look better and are designed for a 3/4 supply return pex line. here is a link to the ones we sell, others have them as well,
http://www.blueridgecompany.com/radiant/hydronic/555/sioux-chief-copper-manifolds
Dan

Professional look for something that will be hidden behind ceiling panels doesn`t bother me that much. I do get the other points. So after the zone manifold you go to a bigger diameter pex till you arrive at the zone header(copper) and after have the pex loops. I didn`t understand why the lines from the zone manifold to the header were in copper (as seen in a few installation manuals)

I'm not sure I understand your question. If you are saying "why don't we use PEX after the zone valve, but before the distribution manifold" then answer is, we do, most of the time. it's ridiculous to run copper any length through a building if you can run pex instead.

Near the boiler though you have many items that require some structural support like pumps, air separators, expansion tanks, etc. hard plumbing is much better for all of that, for weight and also for reduced expansion.

Tx Rob, you cleared it up for me. That does seems logical its just that I had seen diagrams of loop layout where the supply to the header was shown as being copper and I didn`t understand why you wouldn`t just use pex to get there.