Mark Ferrari also teamed up with Ron Gilbert and Gary Winnick (et al) to create a new 2D adventure game called Thimbleweed Park[1] (No affiliation!) - awesome backgrounds by Ferrari!
Palatte shifting and limited color palates were born from the necessity of effeciency. Now he has to use an emulated DOS program to edit them. He uses an experimental web app to display palate shifting projects he created years ago and looks forward to the upcomming release of a pixel editor from the same author.
Additionally, he expresses extensive configuration necessary, mostly disabling anti-aliasing within multiple tools, which makes his process possible in Photoshop. He also has removed the limitation of color palate to make the final product more pleasing, regardless of weight and efficiency, as the concern is minimal on modern hardware.
His technique in Photoshop makes heavy use of the pencil tool one pixel at a time and even falls back to antiquated software (or manual technique) when he needs to implement dithered gradients.
I did not get the inpression that he was happy to be using Photoshop, but that it is currently the best option he has.
It's true he also said sometimes he still has to manually put in pixels, but that seemed to exception to me.
The dithering template only exists because dithering is not a concept in PS; the DOS application has a dedicated dithered gradient tool.