The only concern for 'skin color' in Atharia is that a kingdom might have a certain range. Because the Gods are happy to do whatever they want a child might have a different skin color than their parents (AKA, at the core someone can have white parents with black children, or an Asian parent could have First Nation looking children, it is not a concern to 'make sense' for skin colors for families are). There is no doubting the child belongs to their parents. There is always something that makes it clear.
Each Kingdom, in their second life, had something about them physically changed. It was nothing drastic but it did distinguish the people of each kingdom from each other. A glance would generally let the people who where a person is from.
A side note, just because it is stated 'the kingdom typically...' does not mean PCs have to feel that way unless they want too and/or it fits their concept. Consider the 'typical thoughts' kingdoms have as how the NPCs think.
Choisi Kingdom: Choisi people have the normal hair, eye, and skin color as a typical human. They may not seem like they had any change until one realizes that they are all naturally slender people and they have elf like ears, which are long, slender, and slightly pointed. The features are what they are born with, making it very natural. Choisians are generally short people that vary between 4' and 5'5. As it is come to expect the other races consider the changes to be signs that their choice was the wrong one, that they are corrupted. Choisi Kingdom believes the changes are to help them continue their life of just trucking on and letting things fall as they may, that their choice was correct.
Divinus Kingdom: Those of Divinus Kingdom have faced no changes to their features, at least nothing very powerful. Their appearance is typical of a human, from their hair color to their eye color to their skin tones. There is a very faint glow to their body, that is the most distinguishing part of them that changed since they began their second life. The color of the glow varies from person to person. The height of a Divnitie is what is normal for a human. As with all the races the other kingdoms believe that the choice of Divinus to start over was the wrong one, and the glow to them is a testament of that. It means they are going to fade away and become fallen, or so the kingdoms think. Divinities on the other hand consider their idea to be the right one. They consider the glow to be the light of the Gods, showing their favor for their chosen path.
Luminat Kingdom: The people of Luminat Kingdom have the typical colors of skin and hair that normal humans have but there is almost a ghostly quality to it, as it is paler versions. The eyes of a Luminatie can be any color imaginable, this is their most distinguishing feature of their race. Like all kingdoms, these features are ones they are naturally born with. The people Luminat Kingdom a very varied in heights, they can be as short as 4'5 and as tall as 7'. The other kingdoms find Luminaties to be a little on the creepy side because of the ghost like qualities to them. As expected, the other kingdoms also think Luminat Kingdom is taking the wrong route, that their ghostly quality means they are misguided. Again, as expected, the Luminaties consider the change in their appearance to be the correct one. The ghostly quality means taking the kinder route is the right way.
Santua Kingdom: The people of Santua King have have skin tones that vary between shades of blue, Purple, and green. The hair of a Santuan is typically hues similar to their skin but darker, though, there are some that have what is considered normal human hair colors. Their eye colors are any color under the sun but more often than not ones that compliment their skin tones. All of these are very natural, as in they are born with it. The people of Santua Kingdom are also generally quite tall, the shortest they tend to be is around 5'8 and the tallest is roughly 7'. The other kingdoms often find the appearance of a Santuan to be a little unsettling because they think the appearance is because of their desire to take darker routes to appease the Gods. In the eyes of the other kingdoms, the appearance of Santua Kingdom means they are not taking the right path, that they are forsaken. Santuans, however, believe the changes to their appearance means that they are getting closer to breaking the Curse.
Seat of the Gods: The people that never left the Seat of the Gods have typical human heights, coloring, hair, and eyes. There is nothing unique about their appearance when it comes to distinguishing them from being human. No kingdom has expressed what they think of those that stayed at the Seat of the Gods. Why would they? They aren't willing to potentially offend the people that stay on holy lands.