### 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)
base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_LEFT_CORNER);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_SIDE:
				bit = 3;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_SIDE);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_RIGHT_CORNER:
				bit = 2;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_SIDE);
				break;
			default:
				ERR_FAIL();
				break;
		}
	} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		switch (p_bit) {
			case TileSet::CELL_NEIGHBOR_RIGHT_CORNER:
				bit = 2;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE);
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE:
				bit = 1;
				base_cell_coords = p_position;
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_CORNER:
				bit = 2;
				base_cell_coords = p_position;
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE:
				bit = 3;