I'll focus on the two STID scenes, we see the shuttle entering the shuttlebay and it's right there next to the opening structure of the bay, shadows and all. The ship looks a lot smaller than 725 there...
Not when you consider that for a 725 meter starship, the engineering section would be about 310 meters long -- somewhat smaller than a Nimitz class aircraft carrier
. Even less so when you consider that the length from the back of the shuttlebay to the front of the saucer is only about 530 meters; the rest of the ship's length is the engine nacelles.
It's sort of like the skepticism I get when I tell people the International Space Station
is over a hundred meters wide. It SEEMS a lot smaller when you're only looking at a small part of it. That's because ISS, like Enterprise, is a very large structure composed of several much smaller ones that are themselves much bigger than they look.
Alcatraz is approximately 1 mile away from the waterfront...
It's actually quite a bit farther than that, depending on the direction you're measuring from.