No actual facts or anything about this, just throwing an educated guess at it. My guess is that it doesn't affect the dispatch timings too much, and therefore B&M want to give the rider a more continuous, uninterrupted ride experience.
Strictly, the train only has to have cleared the MCBR before the following train hits the top of the lift hill. On these big B&Ms, the lift hills take a decent portion of time (even on Gatekeeper which is small in comparison to Shambhala) and so adding in dispatch time means that the MCBRs probably don't need to be put halfway through.
Take GateKeeper for example - from dispatch to the top of the lift hill is about 35 seconds, from there to the MCBR is about 60 seconds, and then there's about another 15 seconds before the final brakes. If train-1 leaves the station with train-2 on the brake run waiting (lets just ignore train-3 for now), then I would guess that train-1 is going to be most of the way to the top of the lift hill before the gates are even open to load train-2. By the time train-2 reaches the top of the lift hill I would have reckoned train-1 would be clearing the MCBR, and so train-2 won't need to stop. Repeat of course, for train-3 which is now loading while train-2 climbs the lift hill. Add to that the shortenings of all of these times with the 'once the train has cleared that hill with that speed it's definitely making it up the next hill' logic used commonly these days (the actual name of which escapes me currently), then I think putting them later in the ride has little or no effect of the train efficiency.
Couple that, with the nature of B&M rides and their flow etc, and I would imagine from a designers point of view you'd want to try and keep the tempo of the ride up for as long as you can before putting in an MCBR. I suppose it's a balance between train efficiency and rider enjoyment.
As I said, I'm making ALL of this up, but it seems pretty sensible to me.