No, Apple won’t cover this, not unless they can determine it’s a defect of some sort. What would lead me to believe if this was a defect, is if the chipping was randomized around the aluminum housing surrounding the glass, but it’s not, it’s an exact two positions around the Pentalobe screws, which may or may not have been caused by the skin you appied. Again, something came in contact with it or it was caused by the third-party skin that somehow flaked the aluminum away from the chassis screws. Is this possible it could be a defect? Maybe. But I have my doubts being what I mentioned above.
You could have Apple look at this, and see what they think, if they think it’s a defect, then perhaps they will issue you a replacement device.