"Bright beams" that Nature has wrapped in black are Stella's eyes. In a way, it is also a simile, but every metaphor is a contracted simile (without "like").
There are other literary devices in this passage as well: contrast (black - bright), rhetorical question (one that doesn't have an answer, or an answer is obvious)...
The passage states how the birthmark on Georgiana's cheek causes her to be "countenance even hideous" therefore the answer is B). the birthmark on Georgiana's cheek.
