### 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)
Rect2i texture_region = p_tile_set_atlas_source->get_tile_texture_region(coords);
						Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
						Vector<Vector2> polygon = tile_set->get_terrain_polygon(tile_data->get_terrain_set());
						if (Geometry2D::is_segment_intersecting_polygon(mm->get_position() - position, drag_last_pos - position, polygon)) {
							tile_data->set_terrain(terrain);
						}
						for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
							TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
							if (tile_data->is_valid_terrain_peering_bit(bit)) {
								polygon = tile_set->get_terrain_peering_bit_polygon(tile_data->get_terrain_set(), bit);
								if (Geometry2D::is_segment_intersecting_polygon(mm->get_position() - position, drag_last_pos - position, polygon)) {
									tile_data->set_terrain_peering_bit(bit, terrain);
								}
							}
						}
					}
				}
			}
			drag_last_pos = mm->get_position();
			accept_event();
		}
	}
	Ref<InputEventMouseButton> mb = p_event;
	if (mb.is_valid()) {
		if (mb->get_button_index() == MouseButton::LEFT || mb->get_button_index() == MouseButton::RIGHT) {
			if (mb->is_pressed()) {
				if (picker_button->is_pressed() || (mb->is_command_or_control_pressed() && !mb->is_shift_pressed())) {
					Vector2i coords = p_tile_atlas_view->get_atlas_tile_coords_at_pos(mb->get_position());
					coords = p_tile_set_atlas_source->get_tile_at_coords(coords);