A lot changes between the design phase and what we see on TV. The designers are part of the process, but theirs is the first word, not the final - Ten Forward being TNG's case in point. IIRC, DS9's USS Defiant was designed with landing gear and no shuttle bay, but it ended up the other way around. The USS Voyager was designed with two computer cores and two warp cores but the stories themselves made it explicitly clear they had one of each. The new Enterprise was designed to be 366m, but plans changed and the CG model was made, detailed and sets built/locations used for a much larger 700m+ size.
That's not to say designer input, showing us how they originally conceived everything, isn't fascinating and insightful.