For me, it changes the eyes to the first eye option (the brown eye that is in the top left of the eye options), the eyebrows change to the first eyebrow option, and eye lashes are changed to style 7 every time—for females.
Here is the character I mentioned earlier, and what she looked like after I applied the makeup preset designed for/on her face.
For males, it changes the eyelashes to the second option, but the eyes and eyebrows are also changed to the first option in each of those categories.