The Enterprise-D and NX-01 appear to be correctly scaled. The refit 1701 was designed from the ground-up to be 1000’, and I presume it works at that size with a minimum of fudging...
I suspect you all knew
The 1701-D gets a bit weird when you consider the rim of the saucer was designed as one deck but with the introduction of Ten Forward as the bottom lip of the rim it became a double deck.
The refit 1701 was designed as 305m but the production people built the sets to fit a ship that was at least 355m in length. The cargo bay is too wide, the rec deck too tall, the engine room hallway too long, etc.
The TOS 1701 actually has all the sets that will fit inside a 947' hull (assuming 9' decks for all but one deck in one episode, "Charlie-X") except for the flight deck. That would be where you would scale up the ship in relation to the shuttle.
And this is all before even referring to any tech manuals or blueprints