Again, I'm going to fall back to the example of Twenty Thousand Leagues Under the Sea
. If you were to show people of the 1870's a submarine of today, and described it size, crew complement and accommodations, it's duration between refueling, and the amount of time it could stay submerged, and then asked them to come up with how it was done, what do you think their best guesses would be?
Remember that the best physics of the period (James Clerk Maxwell's Electromagnetic Theory) wasn't even widely adopted yet, so those people would be unable to comprehend any of what we take for granted today.
That is a difference of 135 years. Do you really expect to be able to make better predictions of more than 200 years into the future from where we stand today?
How much coal or oil would it take to power a vessel (without the use of sails at all) back in the late 19th century as far as one of our submarines can go between refueling these days? How much space would that fuel take up? How much less space does the reactor core of one of our subs take up today? Would those people comprehend that difference as anything but pure fantasy?
What ever amount of space you think should be devoted for fuel on this ship, divide it by 10... and that'll still be too much.
We don't know how this stuff works. Later Trek did us all a major disservice by attempting to apply today's ideas to tomorrow. What hasn't changed much in the last few hundred years will most likely not change much in the next few hundred years, but what has changed quite a bit will most likely change even more in the next few hundred years. That is how I'm approaching the interiors and why some aspects I'll leave a little space for and say take a guess
It is funny, the point of using matter/anti-matter was to negate the issue of fuel storage as a problem onboard... but because people think you could burn through it like fuel oil on ships of today, they think a large amount of space has to be set aside for it (mainly thanks to TNG).
As for the three port holes on the front of the primary hull, we never saw what they were for... they were dark in the first pilot, the center one became a navigation light in the second pilot and they were all lit like the other windows by the time of the series. I left the space behind them on deck 6 unoccupied.
Because all the windows we saw from within the ship were rectangular, I'm treating port holes as something else
other than windows.