Ships having a similar configuration doesn't translate into them having the same size. Look at the Coast Guard cutters. They have one basic configuration, but have varying sizes from 29 to 45 meters.
Well, the ship analogy breaks down quickly. Pretty much ALL sea-faring vessels look the same because they operate on water (it's the most efficient design for buoyancy and propulsion). So, whether it's a dingy or a supertanker, it's the same structure.
change between small ships and big ships is the number of windows: those with twice as many decks have twice as many windows. The TMP-E and nu-E, however, have the same
number of windows in identical placements. It was the error on the part of the animators and set designers that caused the "bigger ship" ruckus. They went for what "looks cool," instead of what would realistically fit in the space provided.
Of course, this has been a problem with Trek forever. So, until they actually mention the size of the ship on screen, we can all be happy to believe what we want.