If I had one idea to improve your work from this point of view, why not provide each element in a separate file. Every little item, object, plants, etc ... So it's more easy to manipulate each specific assets in Tiled or other software.
But it's a huge work if you don't work already in separate board for each of your assets. At worst it's up to the game dev to get rid of it via aseprite or photoshop !
😆