the second skin layer is kinda placed lower than the main skin layers grid causing them to not match up
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That's because the second layer is bigger, so it doesn't z-fight with the first layer. Therefore, in order to make it aligned, it would need to have more pixels or not be connected with other faces. It was designed so it is a bit misaligned, but keeps consistency with the lower texture.
This is by design; they're not supposed to be a layer only the existing texture, they're overlaying elements (hat, shirt, sleeves and pants), and not part of the main body. If this was not the case, the hair on your skin also won't appear to stick out.