Option (D)

The problem with the original sentence is separately. Separately is an adverb but in this context it’s not clear exactly which verb it’s modifying. (A) and (B) share the same problem.

(C) and (D) both bring out the parallelism in the sentence, which you can see if you rewrite the sentence: “One benefit of learning to speak a language while learning to read it rather than as/in a separate process is . . . .”. You’ll notice that (D) changes process to the plural processes and undermines the parallelism; the underlined portion should refer to only one process, that of learning to speak a language, in order to create a parallel alternative to while learning to read it.

Hence, (D) is more appropriate.