Yep, elevations are all done by hand. This takes a huge amount of time and it has been my hobby-that-consumes-a-sickening-amount-of-time for as long as that original thread exists... just about 2 years, and there's still plenty to be done.
In fact, I keep retouching parts of the main map as my experience with this technique increases, as I grow in the learning of earth sciences and as I improve the tectonics of Maward. So a lot of the time I spend o this (which isn't much nowadays as I am the father of a 7-month baby) doesn't result in new areas being made.
I did a
video-tutorial some time ago, which you might be interested in. But still, your Atlas Elyden maps are a beauty as they are, vorro, I don't think adding shaded relief would "do wonders".