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.
Another problem with your hypothesis is that the hanger deck of the refit Enterprise
wasn't greatly increased. The ship could accommodate at best two shuttles side-by-side, port to starboard, or vice versa. This was true before the refit, and this was true after the refit. Additional shuttles were stored one deck down, according to a painting of John Eaves. In the new ship, there were two decks of shuttles on one side, and two decks of shuttles on the other side. These shuttles, due to the nature of the design of the bay, were side-by-side, stern to bow, or vice versa. The design of the bay required for a shuttle to leave its allotted space by moving forward, into the direction of the opposite side, then turning to the stern for launch.
For me, I find it telling that the modern military navies of the world tended to avoid having large ships. The rare exceptions were the aircraft carriers. I think this might be attributable to evolutions in ship design and lessons learned from World War II when large ships proved to be the most susceptible to being attacked and destroyed by smaller ships and their auxiliaries, i.e. airplanes. On the other hand, the civilian navies tended towards larger ships. These ships were used for the transporting of people and cargo.