### 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)
TileData *tile_data = _get_tile_data(p_cell);
	ERR_FAIL_NULL(tile_data);
	bool valid;
	Variant value = tile_data->get(property, &valid);
	if (!valid) {
		return;
	}
	Vector2 texture_origin = tile_data->get_texture_origin();
	if (value.get_type() == Variant::BOOL) {
		Ref<Texture2D> texture = (bool)value ? tile_bool_checked : tile_bool_unchecked;
		int size = MIN(tile_set->get_tile_size().x, tile_set->get_tile_size().y) / 3;
		Rect2 rect = p_transform.xform(Rect2(Vector2(-size / 2, -size / 2) - texture_origin, Vector2(size, size)));
		p_canvas_item->draw_texture_rect(texture, rect);
	} else if (value.get_type() == Variant::COLOR) {
		int size = MIN(tile_set->get_tile_size().x, tile_set->get_tile_size().y) / 3;
		Rect2 rect = p_transform.xform(Rect2(Vector2(-size / 2, -size / 2) - texture_origin, Vector2(size, size)));
		p_canvas_item->draw_rect(rect, value);
	} else {
		Ref<Font> font = TileSetEditor::get_singleton()->get_theme_font(SNAME("bold"), EditorStringName(EditorFonts));
		int font_size = TileSetEditor::get_singleton()->get_theme_font_size(SNAME("bold_size"), EditorStringName(EditorFonts));
		String text;
		
		switch (value.get_type()) {
			case Variant::FLOAT: