Returning to the issue of the pylon for a moment, is there anything to say that those (or indeed any of the) round and rectangular "windows" seen on the ship have to actually be windows
Throughout the three years of TOS we only ever saw 3 confirmed windows - two in Conscience of the King
(which were square) and one in Mark of Gideon
(which was more rectangular, but still different from the ones on the Enterprise model).
Additionally, MOG showed us that portholes have both interior and exterior shutters (this feature nicely deals with the discreprencies in interior and exterior window shapes)
So, could some or indeed all of the "windows" seen on the flyby shots each week have in fact been sensors or something? It would certainly explain why there are so many of them in the engineering hull! I mean, shouldn't those engineers be working instead of stargazing?