### 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 (drag_type == DRAG_TYPE_PAINT_RECT) {
		Color grid_color = EDITOR_GET("editors/tiles_editor/grid_color");
		Color selection_color = Color().from_hsv(Math::fposmod(grid_color.get_h() + 0.5, 1.0), grid_color.get_s(), grid_color.get_v(), 1.0);
		p_canvas_item->draw_set_transform_matrix(p_transform);
		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(p_transform.affine_inverse().xform(p_canvas_item->get_local_mouse_position()), true));
		rect = rect.abs();
		RBSet<TileMapCell> edited;
		for (int x = rect.get_position().x; x <= rect.get_end().x; x++) {
			for (int y = rect.get_position().y; y <= rect.get_end().y; y++) {
				Vector2i coords = Vector2i(x, y);
				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;
					edited.insert(cell);
				}
			}
		}
		for (const TileMapCell &E : edited) {
			Vector2i coords = E.get_atlas_coords();
			p_canvas_item->draw_rect(p_tile_set_atlas_source->get_tile_texture_region(coords), selection_color, false);
		}
		p_canvas_item->draw_set_transform_matrix(Transform2D());
	}
};
void TileDataDefaultEditor::forward_draw_over_alternatives(TileAtlasView *p_tile_atlas_view, TileSetAtlasSource *p_tile_set_atlas_source, CanvasItem *p_canvas_item, Transform2D p_transform){