I received a PM asking me to respond to this question.

"have" by itself matches with: I, you, we, and they. In a split between he/she and they, then yes, "have" is plural and "has" is singular. But this sentence doesn't use "have" by itself.

Here's the core structure:
The software <modifier> will [not only X, but also Y]

The [brackets] indicate an idiom requiring parallelism. The part right before that idiom starts should apply separately to each item, X and Y. So we don't have just simple present tense; instead, for Y, it's "will have."

She will have. He will have. They will have. There's no difference between singular and plural now. That eliminates A, C, and E.

D uses "and also" instead of "but also." The idiom is not only X but also Y, so eliminate D.