Well, that is the premise of my entire project with the TOS and TMP refit. For the internal structure my starting premise is that both the TOS Enterprise and the TMP Enterprise follow roughly The TMOST deck layout and Kimball's TMP cutaway poster. With almost no exceptions, Kimball's cutaway is identical to all of Andrew Probert's sketches. Also, the corridor layout for the TMP sets was directly patterned after the TOS sets which were being rebuilt for Phase 2. So other than the movement of certain rooms so other parts of the ship, the internal layout should be identical. In fact, what I found when I laid out both ships according to the cutaway poster, is that the enlargement of the saucer for TMP was exactly one extra ring of cabins. Since we are left with one ring corridor for the set, we don't really get a picture of how the other ring corridors would be laid out. I'm going off of the cutaway where all the doors face inwards except the innermost corridor where Kirk's admirals cabin faces outwards, just like the TOS sickbay sets did.
The changes in the secondary hull make a lot of sense when you place the engine room just after center on the hanger deck. They reposition the engine room forward on a higher deck, the same deck that feeds the warp plasma to the nacells, and install that into an existing part of the secondary hull, and when they tear the old one out it leaves a hole that they just incorporate into the hanger and cargo handling area.
As for the composition of the various pieces of the space frame, I could see where the core frame would be more expensive to manufacture, harder to assemble, and worth stripping off all the plating and rebuilding the ship. To turn back to my frequent example of the USS Constitution / Old Ironsides, her frame was made of live oak which was not supposed to ever be replaced whereas her planks were made of white oak which were made to replace every 10 to 20 years. For the starship, I can see the same thing. A space frame designed to last 50 to 100 years, with Hull plating designed to last at least 20 years. And if they want to change the shape of the ship, they peel off the hull plating and change just the ends of the space frame. In this case mostly adding more. I personally see the neck is being completely replaced as well as the pylons and the engines. And of course the backbone would have had to be rebuilt to accommodate the new engines, but that's a small piece of space frame compared to the entire ship.
The changes in the secondary hull make a lot of sense when you place the engine room just after center on the hanger deck. They reposition the engine room forward on a higher deck, the same deck that feeds the warp plasma to the nacells, and install that into an existing part of the secondary hull, and when they tear the old one out it leaves a hole that they just incorporate into the hanger and cargo handling area.
As for the composition of the various pieces of the space frame, I could see where the core frame would be more expensive to manufacture, harder to assemble, and worth stripping off all the plating and rebuilding the ship. To turn back to my frequent example of the USS Constitution / Old Ironsides, her frame was made of live oak which was not supposed to ever be replaced whereas her planks were made of white oak which were made to replace every 10 to 20 years. For the starship, I can see the same thing. A space frame designed to last 50 to 100 years, with Hull plating designed to last at least 20 years. And if they want to change the shape of the ship, they peel off the hull plating and change just the ends of the space frame. In this case mostly adding more. I personally see the neck is being completely replaced as well as the pylons and the engines. And of course the backbone would have had to be rebuilt to accommodate the new engines, but that's a small piece of space frame compared to the entire ship.