### 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)
color.push_back(Color(1.0, 1.0, 1.0, 0.5));
				Vector<Vector2> polygon = tile_set->get_terrain_polygon(terrain_set);
				if (Geometry2D::is_point_in_polygon(xform.affine_inverse().xform(mouse_pos), polygon)) {
					p_canvas_item->draw_set_transform_matrix(p_transform * xform);
					p_canvas_item->draw_polygon(polygon, color);
				}
				for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
					TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
					if (tile_set->is_valid_terrain_peering_bit(terrain_set, bit)) {
						polygon = tile_set->get_terrain_peering_bit_polygon(terrain_set, bit);
						if (Geometry2D::is_point_in_polygon(xform.affine_inverse().xform(mouse_pos), polygon)) {
							p_canvas_item->draw_set_transform_matrix(p_transform * xform);
							p_canvas_item->draw_polygon(polygon, color);
						}
					}
				}
			} else {
				
				Transform2D tile_xform;
				tile_xform.set_origin(position);
				tile_xform.set_scale(tile_set->get_tile_size());
				tile_set->draw_tile_shape(p_canvas_item, p_transform * tile_xform, Color(1.0, 1.0, 1.0, 0.5), true);
			}
		}
	}
	
	Ref<Font> font = TileSetEditor::get_singleton()->get_theme_font(SNAME("bold"), EditorStringName(EditorFonts));
	int font_size = TileSetEditor::get_singleton()->get_theme_font_size(SNAME("bold_size"), EditorStringName(EditorFonts));
	for (int i = 0; i < p_tile_set_atlas_source->get_tiles_count(); i++) {
		Vector2i coords = p_tile_set_atlas_source->get_tile_id(i);