### 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)
}
		base_control->draw_texture_rect_region(background_texture, Rect2(-background_region.size / 2 - background_offset, region_size), background_region, background_modulate, background_transpose);
	}
	
	if (current_snap_option == SNAP_GRID) {
		Vector2 spacing = tile_size / snap_subdivision->get_value();
		Vector2 offset = -tile_size / 2;
		for (int i = 1; i < snap_subdivision->get_value(); i++) {
			base_control->draw_line(Vector2(spacing.x * i, 0) + offset, Vector2(spacing.x * i, tile_size.y) + offset, Color(1, 1, 1, 0.33));
			base_control->draw_line(Vector2(0, spacing.y * i) + offset, Vector2(tile_size.x, spacing.y * i) + offset, Color(1, 1, 1, 0.33));
		}
	}
	
	for (const Vector<Vector2> &polygon : polygons) {
		Color color = polygon_color;
		if (!in_creation_polygon.is_empty()) {
			color = color.darkened(0.3);
		}
		color.a = 0.5;
		Vector<Color> v_color;
		v_color.push_back(color);
		base_control->draw_polygon(polygon, v_color);
		color.a = 0.7;
		for (int j = 0; j < polygon.size(); j++) {
			base_control->draw_line(polygon[j], polygon[(j + 1) % polygon.size()], color);
		}
	}
	
	if (!in_creation_polygon.is_empty()) {
		for (int i = 0; i < in_creation_polygon.size() - 1; i++) {