### 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)
property_info = PropertyInfo(Variant::BOOL, vformat("physics_layer_%d/polygon_%d/%s", i, j, PNAME("one_way")));
				if (physics[i].polygons[j].one_way == false) {
					property_info.usage ^= PROPERTY_USAGE_STORAGE;
				}
				p_list->push_back(property_info);
				
				property_info = PropertyInfo(Variant::FLOAT, vformat("physics_layer_%d/polygon_%d/%s", i, j, PNAME("one_way_margin")));
				if (physics[i].polygons[j].one_way_margin == 1.0) {
					property_info.usage ^= PROPERTY_USAGE_STORAGE;
				}
				p_list->push_back(property_info);
			}
		}
		
		if (terrain_set >= 0) {
			p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Terrains", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
			for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
				TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
				if (is_valid_terrain_peering_bit(bit)) {
					property_info = PropertyInfo(Variant::INT, vformat("%s/%s", PNAME("terrains_peering_bit"), TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]));
					if (get_terrain_peering_bit(bit) == -1) {
						property_info.usage ^= PROPERTY_USAGE_STORAGE;
					}
					p_list->push_back(property_info);
				}
			}
		}
		
		p_list->push_back(PropertyInfo(Variant::NIL, GNAME("Navigation", ""), PROPERTY_HINT_NONE, "", PROPERTY_USAGE_GROUP));
		for (int i = 0; i < navigation.size(); i++) {