Quote Originally Posted by Scribe
As you say, any potential performance losses are minimal in the worst case to performance gains in best case.
I should mention that there is at least one case in which alpha test hardware is very important: when rendering a shadow map with alpha-tested geometry. Since the shader used for this is almost always very short (one cycle on a lot of hardware), adding a KIL instruction to the shader will cut performance by as much as 50%. The equivalent alpha test is free.

Also, since the alpha test must be supported by the driver for the foreseeable future, I don't think IHVs are going to drop hardware support for it any time soon. It's not difficult to implement in hardware, and it would be silly to burden the driver with recompiling a shader just because the alpha test was enabled/disabled or the alpha function was changed.