The windows on the nu1701 are now only giant because they made the ship to be 300m and only later scaled it to 725m as stated in this thread many times.
Starship scaling occurs a lot in Trek. The most notorious case would be the Klingon Bird of Prey. The 50m sized version in Way of the Warrior from DS9 has tiny tiny windows whereas the 400m version of the Bird of Prey seen in TNG 'The Defector' has fucking massive windows.
there's a HUGE factor being ignored here ... the reason the BoP and other scale issues were so prevalent on the TV series (and remember those are series on limited budgets) is that you'd have had to build new physical models or alter the existing ones.
With models that exist only in the virtual realm, the costs are not exorbitant and the time to alter should not be production-crushing either.
And it isn't like something like this didn't crop up before (and during the physical model era.) On FIRST CONTACT they had finished building the miniature and started shooting it, only to have to stop and revise the model to conform to the practical deflector dish, which Zimmerman was not able to have built to the original specs, necessitating the miniature being physically changed (really put ILM under the gun in terms of shooting ship effects too - they were shooting or reshooting the opening reveal of the -E in late October when I was there, which is pretty late in the game given when it released.)
One of the principal virtues of keeping the ships digital -- and I'm not going to get into the cg vs practical thing again, except to say that precious little spaceship stuff looks all that great to me in whole-cloth CG form -- is to address this exact kind of situation, so why they couldn't really get this fixed (especially given that the movie was finished at least a half-year prior to release), makes me think they just didn't give a shit -- and that suggests that if they mess with the scale for this film, it is because they still don't give a shit.