So call TFF apocryphal and toss it, you'll need other sources to justify the ludicrous window size ...
We don't have to. We're talking about two different ships. Since the TMP refit and the nuEnterprise are two entirely different ships, it doesn't matter if one has bigger windows that the other. However, if one wants to insist that the nuEnterprise windows can't be huge in the TOS timeframe, we can point to the refit-E's arboretum windows, rec deck windows, and officers' lounge windows even if one wants to toss the room seen in TFF. No reason that they must be tiny portholes. And we know that the TOS Enterprise had windows that could be covered sometimes:
http://tos.trekcore.com/gallery/albums/3x16/The_Mark_of_Gideon_121.JPG
http://tos.trekcore.com/gallery/albums/3x16/The_Mark_of_Gideon_123.JPG