I think we're all over-thinking this. The numbers and reaction for Beyond are good enough to have much higher box office. There are three simple reasons for lower box office in my opinion:
1. July release. Something I was worried about. The biggest factor.
2.The "soft" box office this year affected later films in the summer. I wonder if this might even start a trend where Hollywood movies do worse in the USA while the spreading affluence overseas simply makes them the main audience for these films.
3. Non-Trekkies loved Into Darkness. They don't care if it was a Khan reveal. But if they hear stirrings from the trekkie fringes it might make them less keen to see a new film. Some of the word of mouth has been that the movie is sure to please Trekkies. After having 2 less Trekkie pleasing movies, but very crowd-pleasing ones it may be keeping some of those on the fence from seeing it.
I'm still happy it got made and it may wind up being one of my most re-watched films.
RAMA
The July release is definitely a factor! The previous two movies were helped by their May releases as movies that open in May, June and very early July tend to do higher box office. Late July is seen as the start of dump months.