### 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)
overlap = 0.25;
				break;
			case TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE:
				overlap = 0.0;
				break;
			default:
				break;
		}
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_half_offset_corner_or_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_half_offset_corner_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		} else { 
			return _get_half_offset_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		}
	}
}
#define TERRAIN_ALPHA 0.6
void TileSet::draw_terrains(CanvasItem *p_canvas_item, Transform2D p_transform, const TileData *p_tile_data) {
	ERR_FAIL_NULL(p_tile_data);
	if (terrain_bits_meshes_dirty) {
		
		terrain_peering_bits_meshes.clear();
		for (int terrain_mode_index = 0; terrain_mode_index < 3; terrain_mode_index++) {
			TerrainMode terrain_mode = TerrainMode(terrain_mode_index);
			
			Vector<Vector2> polygon;
			if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
				polygon = _get_square_terrain_polygon(tile_size);
			} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {