Boy Simon, I am confused -
the new cylinder Mac Pro has no slots. You take the Tnunderbolt port and go into the Netstor, and INSIDE the Netstor is where you put the ix card - so the 16 drives connect to the internal connectors. The ix has one external port for SAS expansion.
If it only had external ports, how would you get it to work with the Netstor and the new cylinder Mac Pro ?
Advanced Format (4K sectors) is what you want. It's better if you can use it. Not all cards support it, which is why the drives support 512 byte emulation. You don't want to be using that since it'll be worse than native 512bytes. So long as the card claims to support advanced format, you're good.