Let me explain stuffs:
- Issue 1: in the context of one pattern/shape, a 2D tile always maps to a 3D tile, so when you modify the solid 2D tile which is used in many positions, 3D tiles mapped to that 2D will all changed
Return to the main problem: because the background city pattern contains a solid 2D tile so the background shape incorrectly contains that building part which is also a solid tile. That's that reason. Solution, play with pattern restriction (default is 99 tiles in x and 99 tile in y).With background city pattern you should set restriction x to 1, the background city will be cut into shapes with width of 1 tile.
After that you should create a pattern composing of the solid tile and the lower brick tiles (in tile mode). Or merge brick shape with the shape of solid tiles.
Shape will be segmented correctly after that because the underlying mechanism in segmentation is: shape will expand as big as possible as long as there is at least one pattern compatible with it (compatible mean pattern 2dtile set is the super set of shape 2dtile set)
- Issue 2: the reason is that game uses "transparent color - value 0" for the windows. The empty part corresponds to empty 2d tiles - "solid" tiles with all transparent color pixel. That special kind of tile is currently filtered out before the segmentation process. That's why we see the emptiness here - the default semantic of this kind of tile in most cases.
Because of the lack of color in nes system in some case like this case, the game uses transparent color as an additional one, that behavior cause issue. I will try to see how to handle this issue.