When you apply a photo-matched texture to a surface, the actual image is still rectangular, but SU adds some information to the image/surface that tells it how to deform the rectangle so that it maps properly. (Probably the relative x,y of each corner).
Enscape does not understand all of these transformations and so just does it's best. (Probably Enscape can't access this info through the SU API)
When you "Make Unique", it converts the stretched image to a flat rectangle image of just the right size to fit the surface - Enscape likes this and can show it just like every other texture.