### 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)
RID ci;
					
					if (prev_ci == RID() || prev_material != mat || prev_z_index != tile_z_index) {
						
						ci = rs->canvas_item_create();
						if (mat.is_valid()) {
							rs->canvas_item_set_material(ci, mat->get_rid());
						}
						rs->canvas_item_set_parent(ci, canvas_item);
						rs->canvas_item_set_use_parent_material(ci, tile_map_node->get_use_parent_material() || tile_map_node->get_material().is_valid());
						Transform2D xform(0, rendering_quadrant->canvas_items_position);
						rs->canvas_item_set_transform(ci, xform);
						rs->canvas_item_set_light_mask(ci, tile_map_node->get_light_mask());
						rs->canvas_item_set_z_as_relative_to_parent(ci, true);
						rs->canvas_item_set_z_index(ci, tile_z_index);
						rs->canvas_item_set_default_texture_filter(ci, RS::CanvasItemTextureFilter(tile_map_node->get_texture_filter_in_tree()));
						rs->canvas_item_set_default_texture_repeat(ci, RS::CanvasItemTextureRepeat(tile_map_node->get_texture_repeat_in_tree()));
						rendering_quadrant->canvas_items.push_back(ci);
						prev_ci = ci;
						prev_material = mat;
						prev_z_index = tile_z_index;
					} else {
						
						ci = prev_ci;
					}
					const Vector2 local_tile_pos = tile_map_node->map_to_local(cell_data.coords);
					
					real_t random_animation_offset = 0.0;
					if (atlas_source->get_tile_animation_mode(cell_data.cell.get_atlas_coords()) != TileSetAtlasSource::TILE_ANIMATION_MODE_DEFAULT) {