It doesn't have to be. The Bridge has been consistently refered to as deck one on the Enterprise, Engineering Deck 36 and that easily corresponds to the proper location on the MSD for the Galaxy.
Voyager has managed to mention EVERY SINGLE DECK listed on the MSD 15 total no room for extra side decks.
Every MSD would be instantly wrong under such a theory whether canon or not just to accommodate one wrong MSD. That doesn't seem like a rational determination.
As noted, there is no law of physics prohibiting Starfleet from using irregular deck numbering on occassion. After all, computerized turbolifts and helpful labels can take anyone to the right place. Even if you don't believe this, then it is better to believe there is no Deck 5 (= error) than to ignore the ubiquitous four-deck layout.
Belief should be dictated by logic.
Three sources contradict the Okuda gram. Dialogue, the vessels external design and Turbo lifts display.
As for what else the "windows" could possibly be - I don't know, but there is no canon proof they are windows either.
That's not true in ever sense of every other model they are arranged by levels and emit white light just like every other ship human and alien. So once again it would be irrational to suggest that every such representation of understood logic be thrown out just because of one oddity of a MSD.
>
Modelmaker Tony Meininger probably did intend them to be windows, because the 170m size had been established before the model was built, by VFX supervisor Gary Hutzel who worked closely with Meininger, but we must somehow reinterpret them in light of the MSD.
That is purely unrestrained conjecture.
If the model was created independently from the the dimensional figure and the MSD t's illogical to attempt to assume they must be coherent. Evidience clearly shows none of the variables are consistent except that the MSD is wrong.
And no, we cannot assume the ship is 170m long with excessively spaced four decks, because that's worse than merely theorizing they aren't labeled regularly or that "Deck 5" is an error. Why wouldn't the omnipresent MSD show all that missing space? Why distort the scale and the placement to such an extent? That is not a best-fit solution.
Quite simply the MSD has been proven wrong. For Defiant it's just not a bench mark for consistency. The scale isn't consistent in canon in any stretch of the word either. We've even seen entirely wrong shapes to defiant in it's MSD's which were abandoned. We have considerable more play in the Defiant's internal arrangement than in any other ship because there is only one consensus...the Okudagram is wrong. Thus all the consistent evidence for Defiant's internal arrangement becomes a primary undiminished canon. The MSD isn't sacred. Once proven wrong it's useless to us like any map if a highway that should be there isn't there then it's reliability is shot.
the external arrangement is far more consistent despite vagueness of CGI perception they always go back to the model which all CGI was interpreted from. There is nothing new except for escape pod hatches that weren't there and shuttle bay doors that weren't previous present. One time occurrences.
I say completely abandon the MSD Okuda made. (I think he would) and redesign the ships interior to properly match the external arrangement as is done in engineering and drafting instead of independently as was done with this ship. It is better to correct than to miss lead with false designs that are not in accord with anything else.