### 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)
ERR_FAIL_INDEX(p_index, (int)polygons.size());
	polygons.remove_at(p_index);
	if (polygons.size() == 0) {
		button_create->set_pressed(true);
	}
	base_control->queue_redraw();
}
void GenericTilePolygonEditor::clear_polygons() {
	polygons.clear();
	base_control->queue_redraw();
}
void GenericTilePolygonEditor::set_polygon(int p_polygon_index, Vector<Point2> p_polygon) {
	ERR_FAIL_INDEX(p_polygon_index, (int)polygons.size());
	ERR_FAIL_COND(p_polygon.size() < 3);
	polygons[p_polygon_index] = p_polygon;
	button_edit->set_pressed(true);
	base_control->queue_redraw();
}
Vector<Point2> GenericTilePolygonEditor::get_polygon(int p_polygon_index) {
	ERR_FAIL_INDEX_V(p_polygon_index, (int)polygons.size(), Vector<Point2>());
	return polygons[p_polygon_index];
}
void GenericTilePolygonEditor::set_polygons_color(Color p_color) {
	polygon_color = p_color;
	base_control->queue_redraw();
}
void GenericTilePolygonEditor::set_multiple_polygon_mode(bool p_multiple_polygon_mode) {