In the past I made screen-shots like that for CaesarIII in which I cropped the out "pause" box. When I got to the top of where the view could be scrolled to I would judiciously place the "pause box" into the black background area that is not part of the map, since in CaesarIII the map is at a diagonal to the screen. I would then use a paint program to paint over the "pause box" before assembling that with all the other cropped screen-shots to make the master image. Such a technique would work for Pharaoh so long as nothing which would change its appearance (such as the animation of a building, the growth cycle of a farm or a walker/animal sprite) is located at the very upper-most edge of the screen, beneath the "pause box;" otherwise un-pausing the game (to remove the "pause box" from obscuring something on-screen) could result in two different screen-shots which might not be precisely overlayed.
Since I often build Pharaoh cities right up to the edge of the map (since I like to build for sheer size) this have proven a problem for me in trying to create screen-shot maps of my Pharaoh cities like I used to do for CaesarIII cities. However I notice in that picture the top edge contains only open land which does not change due to animations and the only sprites are of some immigrants and a caravan without buildings in the area they would be screen-shotted with whose animations could very when the game is un-paused.
Long story short I think they oriented the map in a very clever way to get around my conundrum.
I hope that wasn't toooooo complicated an answer.