If you bought the assets, you probably cannot redistribute them, even if you are just posting them here to ask for help. Please check the license for the assets and whether you can redistribute them, and if you cannot, then please remove the images or get one of us admins to remove it. Posting material you are not allowed to redistribute is against forum rules (if nothing else, for legal reasons).
Regardless, to answer your question: It looks like the tileset is for RPG Maker, and all of the tiles are on a consistent grid size. In software like RPG Maker, you use multiple tilesets with differing Z-indexes to place details on top of each other, making the tiles with cutouts work as expected. In Godot, I would use a base tilemap and a details tilemap, where the base tilemap has the main structure, and the details tilemap has things like the windows, doors, etc.