Yeah, I know. The scales of both the Vengeance and the Enterprise change several times. In the first movie, when Kirk is looking up at the ship being built you can see several people on scaffolding which allows for a size comparison. I calculated that it was somewhere between 300 and 400 meters long. Then of course there's the shuttlebay shot which they scaled it up for. After that it seems to revert back to its original size and stay that way for the whole movie. You can even see that the rim of the saucer is only two decks thick.
In STID, it also seems to be around 350 meters or so. And the Vengeance is twice its size, until the crash scene where it seems to grow. Since it seems to be rather inconsistent I just choose the more plausible option of having the smaller sizes.
You've got it somewhat backwards - the new Enterprise was shrunk down for one shot over the shipyard (to fit the location used), but even then was detailed to be 725m - those poor workmen would never fit on the exposed decks!
The bridge, lobby behind (plus number of decks seen + spacing between), engine rooms and shuttlebay wont possibly fit inside a 350m Enterprise. See the Starship Size Argument and Bridge Set Plans threads in STXI for more details. Basically, for the ship to be 350m you have to ignore virtually the entirety of both Star Trek and Into Darkness.
...and the Vengeance is twice THAT size