Intel's Iris Graphics Boost 13-inch Retina MacBook Pro GPU Performance by 50% or More

The site claims the GPU on the Mac Pro is placed on an independent daughter card with a proprietary connection, which would make sense as it would make warranty-repairs of broken GPUs significantly easier. There is no indication if or when third-party graphics cards could be released for the new Mac Pro, but the new device is scheduled for release in December of this year.

A similar system is used in the MacBook Air's SSD flash storage. In 2010, Other World Computing released aftermarket SSD upgrades for the MacBook Air, allowing larger SSD options than Apple's 256GB maximum -- for a significant price. The MacBook Air uses a proprietary SSD connector and board, but OWC was able to design replacement storage options for the computer.

Apple did specify that RAM in the new Mac Pro would be user replaceable, but said nothing about the graphics cards. It's likely that the graphics cards, if it's even possible to replace them, would not be an Apple-approved user replaceable part and could affect the product's warranty, much like the aftermarket SSD replacement in the MacBook Air.
Source : Mac Rumors