"Only the nvidia specific features don't run well on AMD hardware" That makes no sense then.

If Nvidia specific features are standardized in the source code of a video game and cause poor performance for AMD GPUs, than it ruins the performance for AMD GPUs.

GameWorks is a set of proprietary libraries, distributed by Nvidia, used to implement common DirectX 11 functions. Developers that use these libraries cannot share the source code with AMD for optimization because it's licensed. AMD GPUs rely on source code optimization and without that code to share with AMD during Killing Floor 2's development, it's gonna perform worse on AMD equivalent GPUs.

Look at WatchDogs. Ran like crap on both GPUs, but it is worse for AMD users. Far Cry 4, which has GameWorks, has Nvidia’s suggested card a GTX 680 while an R9 290X is suggested for AMD users. What? That's a massive performance gap between the two cards.

For Unity, NVIDIA GeForce GTX 780 is recommended for Nvidia users, while a AMD Radeon R9 290X is AMD users.

The AMD Radeon R9 290X has a 2.2x better score on the 3DMark 11 graphics score, has 35% more graphics memory or 1GB more, has a 35% or 128 bit wider memory bus, and has a 133 MHz higher clock speed,....but is equivalent to performance with GTX 780?

Nvidia is trying to crush AMD GPUs with software optimization, not hardware performance. Gameworks is Nvidia's software optimization.