In X2, Mystique transforms into Jean Grey. When Wolverine lifts her cloth, she has scar at same place where he had injured Mystique in X-Men's 1st movie.

So it is clear that even though Mystique can't see people under clothes, she can transform into same body as that of target. But she can't replicate details like injury marks, birth marks until she sees them by her own eyes. In this case, she retains her own physical features to body parts which are not visible or covered (say using clothes). She can even replicate the skin tone if we go by this scenario.

The clothes and accessories are created out of biological cells from her own body.