Well.. I can't tell you anything specific about this, especially the author's intent, BUT.. the artist Mike Schley is a member here. He might have some notes, but my initial reaction is the same as yours on the whole portcullis thing... I say, just make your map the way you want it... you could always alter the adventure text a bit during game play if you make area nine as it appears in this map.
EDIT: on second look, the 2nd floor (top map) clearly shows a structure above the portcullis. There is no way to know the height of the structure, but it is very likely more than enough to house the portcullis on an up/down orientation assuming door height = less than floor to ceiling height on both the 1st and 2nd floors.