I think I kind of get it then...but still don't know why they just cant put in and incorporate that 680gtx~
Two reasons:
1. Because Apple makes complete systems. They are not a BTO parts supplier.
When a redesigned Mac Pro ( not a minor speed bump ) arrives there will be new video cards. That doesn't happen every year so the default set of cards don't appear every year. When the 2013 Mac Pro arrives it should bring new cards. ( Probably a mix of both AMD and Nvidia this time but probably only one will be the default for all the configs )
Is it possible for Apple to change core principles and becomes a parts remarketer? Yes. Probable? No, there is about zero financial incentive to do so.
2. This one has two sub parts.
a. Because the aftermarket PCI-e GPU card market is very small so the 3rd party vendors do not rush to provide cards. Apple doesn't stop them. But it isn't going to bribe to do it either. There is only one, relatively low volume Mac model that can take these cards so they sell in relatively very low volumes.
Some vendors take a stab at it. But....
b. there is a cottage industry of tweaking Windows/BiOS oriented cards into Mac Pro compatible cards ( with varying degrees of functionality). All the more so if a vendor does much of the heavy lifting ( the ROMs will be cloned and/or reverse engineer and the vendor will see less cards sold). Since it is already a small market and the cottage market makes it even smaller, even fewer vendors want to take a crack at a 3rd party offering.
Things are getting better as the Windows PC industry starts to deploy UEFI systems that stop masquerading as principally BIOS ones. Likewise Apple is tweaking their EFI to follow the updates EFI graphics layer. The gap between Mac and Windows boot environments is closing.