Gameworks and Mantle are different. Mantle is a new low overhead API that allows developers to optimize their game and create new experiences using AMD hardware. The code is available to all, the developers and AMD share the source - and as your pointed out, Mantle only runs on AMD hardware right now.
Gameworks is different. Gameworks libraries are precompiled blobs that the developer can't adjust, can't change, can't see how they work to tweak for their use. AMD can't optimize or fix bugs, it's all dark code, no way to know why the code doesn't run as fast on an AMD card as it does on an NVIDIA one. Is it a problem with a driver? Is it problem with how a shader is compiled? Is it code deliberately written to overflow a buffer or stall out a hardware cache?
Both companies are optimizing the experience for the users - this is expected and encouraged by consumers in their reactions of drivers, game updates, new releases. AMD's method with Mantle and the freely available technologies like TressFX - which runs just as well on NV hw as it does AMD hw - is intended to move the industry forward, give the developers the tools and access they want to make great games.
Watch Dogs performance looks like NV are going after performance wins not by optimizing to their hardware or improving their drivers, but by blocking the ability of AMD to optimize on the same codepath. As Techreport states:
Forbes said:
"It's evident that Watch Dogs is optimized for Nvidia hardware," Evangelho writes in his story, "but it's staggering just how un-optimized it is on AMD hardware." Evangelho also links an older article by ExtremeTech. That article made a similar observation about Batman: Arkham Origins, and it similarly pinned the blame on GameWorks.
We've seen in our own testing how AMD graphics cards can underperform in some GameWorks-enabled games, including Batman: Arkham Origins and Assassin's Creed IV: Black Flag, so Evangelho likely isn't wrong there. For whatever reason, some GameWorks titles do seem to run poorly on Radeons.
http://techreport.com/news/26515/amd-lashes-out-at-nvidia-gameworks-program
Of course, I work for AMD so I am biased in this matter - but look at all the sites examining performance and their conclusions. Is it sour grapes on AMD's part? Or is it a problem as claimed by Extremetech - gamers are being blocked from the full potential of their hardware because of Gameworks? No matter which way you think, I think it's in everyone's interest that the details are discussed and the problem exposed.