That brewery is highly unrealistic, Abrams should have used money to actually design an engineering set instead of using a beer brewery, he even left the brewery's skylight windows in the top of the engineering section. I'm looking at the brewery they used on google earth and the brewery itself could fit in a ship that was smaller than 725 meters. The building with all the tanks and pipes is smaller than the sorting and packaging building. The eastern most part when measured from the last building to the street is 1480 feet. The trouble is we never get any kind of technical graphic that explains everything, That being said, I'm just going to let my imagination guess since their sets do not connect to each other to form a ship that people can accurately figure out.
IMO the engineering sections in Star Trek
and Into Darkness
are the same as those we saw in TOS, but on a far larger scale:
There is no chance that the brewery would fit into an Enterprise with a 30m wide engineering hull, as would be the case on a 366m/1200ft Enterprise. It would need to be far larger.... say, 725m/2380ft?
As for where everything fits, I made this way back at the start of the thread. Again, I think the only reason you cannot figure it out is because you're working from a faulty assumption - that this Enterprise is about the same size as the old one (300ish meters), when the makers of the film have said and shown repeatedly that their Enterprise is around 725m long.