Windows were added over Jefferies objections in the second week of November 1964 (and Jefferies had to answer to at least three other people on production issues), the scale of the window in Pike's room is fine considering that it was closed
How does closing a window make it smaller? Or bigger? Or... what?
Anyway, I don't remember completely the original version except that the window was on a curved wall that was implied to be either the dome under the bridge (unlikely considering the hallway outside) or somewhere in the secondary hull (a bit more likely considering the hugeness of the room). Either position would still make the Cage Enterprise considerably smaller than the final version.
The windows in Kirk's room were a problem and were eventually covered over because of it.
I figured, since by then they had revised the scale of the ship to be larger than before and the windows didn't fit anymore. You'll notice they did the exact same thing in STXI, with those "communications stations" in the corridor parked in front of ovoid and circular features that were almost certainly meant to be saucer rim windows; they no longer fit the upscaled version, so star fields were omitted and they were left as featureless white lights.