It's only Dark Castles and Golden Towers that have odd placements I think. (and settlers headquarters, but you can't get them anymore)
Unfortunately the building placement you see in game is not as it seems, the solid green squares are actually where 4 squares intersect:
(I have also highlighted where the grid lines up with the wells.)
The size is also a reason a lot of higher level players don't use dark castles, you can either use a dark castle for 100 population with it using a ~4x4 grid, or you can place 4 nobles and upgrade them to lvl3 to get 200 population from almost the same land usage.