1) Yeah, I've painted 2D bitmap navmeshes in other games, or made them by hand for 3D scenes out of polygons. It's not that hard, just dull and timeconsuming.
2) They render a depth pass for this. (basically, a value of a pixel in the image is the depth on the Z axis it has in the scene. Imagine it like if you took a sculpture and measured the height of every tiny point of it, then coloured a correspoinding pixel in the depth map with the appropriate shade of gray)
3) Diffuse and spec maps, which are also passes in the render. (Josh talks about this in the dev conference video.)
1) I may be wrong, but as far as I know, painting navmeshes in Unity isn't possible unfortunately. There are alternatives to Unity's navmesh system, but they cautiously never show how their system works on uneven terrain. I remember even someone from PoE's staff complained about Unity's navmesh being shit.
2) So they build a kind of height map, if I understand you correctly? Maybe, but a custom tool needs to be used for that, no? That's what "not easy" means.
3) A custom tool for that too, no?