### 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)
undo_redo->create_action(TTR("Clear Polygons"));
			undo_redo->add_do_method(this, "clear_polygons");
			undo_redo->add_do_method(base_control, "queue_redraw");
			undo_redo->add_do_method(this, "emit_signal", "polygons_changed");
			undo_redo->add_undo_method(this, "clear_polygons");
			for (const PackedVector2Array &polygon : polygons) {
				undo_redo->add_undo_method(this, "add_polygon", polygon);
			}
			undo_redo->add_undo_method(base_control, "queue_redraw");
			undo_redo->add_undo_method(this, "emit_signal", "polygons_changed");
			undo_redo->commit_action(true);
		} break;
		case ROTATE_RIGHT:
		case ROTATE_LEFT:
		case FLIP_HORIZONTALLY:
		case FLIP_VERTICALLY: {
			switch (p_item_pressed) {
				case ROTATE_RIGHT: {
					undo_redo->create_action(TTR("Rotate Polygons Right"));
				} break;
				case ROTATE_LEFT: {
					undo_redo->create_action(TTR("Rotate Polygons Left"));
				} break;
				case FLIP_HORIZONTALLY: {
					undo_redo->create_action(TTR("Flip Polygons Horizontally"));
				} break;
				case FLIP_VERTICALLY: {
					undo_redo->create_action(TTR("Flip Polygons Vertically"));
				} break;
				default: