### 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)
if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
						_set_painted_value(p_tile_set_atlas_source, coords, 0);
						picker_button->set_pressed(false);
					}
				} else if (mb->is_command_or_control_pressed() && mb->is_shift_pressed()) {
					drag_type = DRAG_TYPE_PAINT_RECT;
					drag_modified.clear();
					drag_painted_value = _get_painted_value();
					drag_start_pos = mb->get_position();
				} else {
					drag_type = DRAG_TYPE_PAINT;
					drag_modified.clear();
					drag_painted_value = _get_painted_value();
					Vector2i coords = p_tile_atlas_view->get_atlas_tile_coords_at_pos(mb->get_position(), true);
					coords = p_tile_set_atlas_source->get_tile_at_coords(coords);
					if (coords != TileSetSource::INVALID_ATLAS_COORDS) {
						TileMapCell cell;
						cell.source_id = 0;
						cell.set_atlas_coords(coords);
						cell.alternative_tile = 0;
						drag_modified[cell] = _get_value(p_tile_set_atlas_source, coords, 0);
						_set_value(p_tile_set_atlas_source, coords, 0, drag_painted_value);
					}
					drag_last_pos = mb->get_position();
				}
			} else {
				if (drag_type == DRAG_TYPE_PAINT_RECT) {
					Rect2i rect;
					rect.set_position(p_tile_atlas_view->get_atlas_tile_coords_at_pos(drag_start_pos, true));
					rect.set_end(p_tile_atlas_view->get_atlas_tile_coords_at_pos(mb->get_position(), true));