In the second game, we learn that Inkies are made of sentient ink and are assembled using Graydian labor. Where does that ink come from? Apparently from the bodies of Graydians themselves, generated from their despair and sorrow from being deprived of color and excitment, as we learn in the first game. The process to extract that ink (herding Graydians onto a rickety old carnival ride and forcing the ink out via centrifugal force) also probably counts.
Also, in both games if you roll over a Raydian while inked, it'll flatten and then burst into nothing. This has no bearing on your post-level Raydian liberation total in the second game.
"Comrade Black affirms that inkboarding is not torture."
The creepiest part of the second game, is the part where you explore the Ink Fabricator. During the level, a inkie mutant was created, and it's somewhere in the factory. The worst part is the silence, which makes it feel like the mutant is just going to appear out of nowhere.