I know Orci fequently chimes in the trekmovie.com comment sections. Has he made any comments since Beyond opened?
When asked what he thought about the movie he just said 'fun'.
Then he made a comment about how, in spite of Pegg&co not reading his script, there are similarities like the (initial?) s/u break up, that massive starbase, the search for an ancient artifact and the 'bees' ships.
I think the producers/studio that read his script might have suggested some things they liked (like s/u's arc about his conflict etc) to Pegg&co. The scripts are owned by the studio anyway and they can do what they want. Anyway, if his script was similar about some aspects to stb, then I think the story they have for trek 4 can't be the original story orci had for trek 3 but probably it was the plan b those writers had when the studio didn't like the first script (Orci once said that they did have a second story too) They'll have to adapt whatever they have already with what happened in this movie (can't tell the same stories twice).
Search for his comment here
http://trekmovie.com/2016/07/21/star-trek-beyond-spoiler-discussion/#comments