That tile set is from an isometric engine, where "tall" tiles are the norm -- as for why the house is cut up, I can't really say, but without looking too closely at it I would postulate that it might be done so that portions of the house can be mixed-and-matched to provide more variety to the houses in the village.
Imagery doesn't have to be consistent so long as the engine and data formats can deal with it.
It fits more easily into the tileset that way. Observe:
In tilesets (spread out to grab rectangles of pixels):
In games (rectangles of pixels overlapping):
(Pardon my uneven red lines that don't properly line up)
How are you going to separate the tiles properly, if the middle chunk actually goes one row lower (one half-tile lower) than the others? The chunks of the house on the left and the right are half-obscured by the center chunk of the house.
Remember with isometric tiles, every other row is offset by half a tile both vertically and horizontally. So if two pieces of tile fit together on two seperate rows, the one tile behind the other tile will be half obscured.