I suspect there is not perfect answer. Each must make his own choice of which details he honors and which he sacrifices.
My own approach was to hold on to Jefferies stated 947' length, and his cross section showing the hangar aft of the pylons.
I could never get over the Franz Joseph depiction of the pylons just sticking on to the exterior skin of the hull. I realize that the warp engines' main function is not to generate thrust, but just taking into account the amount of shaking around and even atmospheric friction the ship encounters they must have a pretty robust connection.
I also took to heart Jefferies' location of Engineering on the Phase II cross section. It is still right in front of the hangar (even though the pylon connection points have changed during the refit).
All the above led me to the conclusion that the hangar deck model, whether actually forced perspective or not, was built as it was, primarily, to fit a camera into its end and still have room to pour light in around it. In short I decided not to take too literally what the miniature was
, and instead focussed on how the miniature looked.
Admittedly, the hangar that meets all the above requirements does not look exactly like what we saw onscreen. Only a very wide angle virtual lens, placed outside the physical confines of the hangar, can give you similar views. But then, again, the camera that filmed the actual footage was outside that mythical "fourth wall" looking in, too.
Finally, one further point you might consider if you decide to make the hanger as long and conical as the miniature: Where are the windows we see from the outside of the secondary hull if there is only a little wall space between the hangar interior and interior? Unless there is an increasing amount of space between the walls as you go forward, there is apparently no way they can be windows at all.
The amazing thing about all of this, is that the calibre of work that Jefferies and the rest of the production crew of TOS accomplished still inspires and rewards efforts like these forty years later. The quality of work done by fans like Petri, Blssdwlf, Warped9 and many others is nothing short of wonderful.