### 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)
background_texture = p_texture;
	background_region = p_region;
	background_offset = p_offset;
	background_h_flip = p_flip_h;
	background_v_flip = p_flip_v;
	background_transpose = p_transpose;
	background_modulate = p_modulate;
	base_control->queue_redraw();
}
int GenericTilePolygonEditor::get_polygon_count() {
	return polygons.size();
}
int GenericTilePolygonEditor::add_polygon(Vector<Point2> p_polygon, int p_index) {
	ERR_FAIL_COND_V(p_polygon.size() < 3, -1);
	ERR_FAIL_COND_V(!multiple_polygon_mode && polygons.size() >= 1, -1);
	if (p_index < 0) {
		polygons.push_back(p_polygon);
		base_control->queue_redraw();
		button_edit->set_pressed(true);
		return polygons.size() - 1;
	} else {
		polygons.insert(p_index, p_polygon);
		button_edit->set_pressed(true);
		base_control->queue_redraw();
		return p_index;
	}
}
void GenericTilePolygonEditor::remove_polygon(int p_index) {