When I was building out a largish-town map, I decided it would be more efficient to fully design and decorate the houses on a blank area to the side and paste them in place afterwards, rather than awkwardly trying to tweak them in the actual environment. However, I found afterwards that the semi-transparent tiles I copied, such as roof corners and fences, overwrote the terrain with transparent tiles, and I could not redraw the terrain under them without overwriting the decorative element or shadows drawn on top, which was part of what I was trying to avoid in the first place.

I could fill in my assembly area with the default terrain, but if I choose, for instance, to change how a dirt path connects to the house, I have the same issue of having to fish through the tile set to replace things, and it wouldn't help the buildings that I've already built out.

I found this produced a lot of issues when trying to furnish indoor maps, for example, wanting to change which carpet to use in an area, or when trying different decorative objects on a table, having to replace the floor tile, table tile, and object in order rather than just swapping the object on the top layer.

While there's workarounds for all these issues if you put the time in and keep fishing back through the tiles to rebuild stuff, I've found that all together they've been eating up a ton of time during the polish stage, and could become a huge headache if I have to fill out the entire game like this.