### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
}
					p.pop_front();
				}
			}
		} else if (what == "shapes") {
			Array p = p_value;
			for (int i = 0; i < p.size(); i++) {
				CompatibilityShapeData csd;
				Dictionary d = p[i];
				for (int j = 0; j < d.size(); j++) {
					String key = d.get_key_at_index(j);
					if (key == "autotile_coord") {
						csd.autotile_coords = d[key];
					} else if (key == "one_way") {
						csd.one_way = d[key];
					} else if (key == "one_way_margin") {
						csd.one_way_margin = d[key];
					} else if (key == "shape") {
						csd.shape = d[key];
					} else if (key == "shape_transform") {
						csd.transform = d[key];
					}
				}
				ctd->shapes.push_back(csd);
			}
		} else if (what == "occluder") {
			ctd->occluder = p_value;
		} else if (what == "navigation") {
			ctd->navigation = p_value;
			/*