Those *_ap.dds files contain the albedo maps (RGB channels) and paint mask (alpha channel).
The albedo map contains only the relative brightness data of the surface (no baked in shading) and gets tinted to a color by the material parameters (and then shaded in real-time by the render pipeline). The paint mask is so any finely painted details don't get tinted as well. Take a look at the new Incursus textures to see what is going on better.
Also what is changed is the *_pgs.dds files are now *_pgr
.dds files. Those contain the factional paint masks, glow map, and the new "roughness map" (instead of the old specular map). The roughness map describes the microtexture of the surface to the PBR render pipeline so it can calculate real-time specular highlights and additional shading.
This guide helped me get my bearings on PBR - http://www.marmoset.co/toolbag/learn/pbr-practice
Be aware that Physically Based Rendering is more of a concept than any kind of specification. CCP's implementation in Eve is a bit simpler than what that guide describes, but the core concepts are there.
In general, PBR is about defining how a surface behaves
with light, rather than describing what it looks like - you let the render figure that out based on the environment.