### 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)
int font_size = TileSetEditor::get_singleton()->get_theme_font_size(SNAME("bold_size"), EditorStringName(EditorFonts));
	for (int i = 0; i < p_tile_set_atlas_source->get_tiles_count(); i++) {
		Vector2i coords = p_tile_set_atlas_source->get_tile_id(i);
		if (coords != hovered_coords) {
			TileData *tile_data = p_tile_set_atlas_source->get_tile_data(coords, 0);
			if (tile_data->get_terrain_set() != int(dummy_object->get("terrain_set"))) {
				
				p_canvas_item->draw_set_transform_matrix(p_transform);
				Rect2i rect = p_tile_set_atlas_source->get_tile_texture_region(coords);
				p_canvas_item->draw_rect(rect, Color(0.0, 0.0, 0.0, 0.3));
				
				p_canvas_item->draw_set_transform_matrix(Transform2D());
				Rect2i texture_region = p_tile_set_atlas_source->get_tile_texture_region(coords);
				Vector2i position = texture_region.get_center() + tile_data->get_texture_origin();
				Color color = Color(1, 1, 1);
				String text;
				if (tile_data->get_terrain_set() >= 0) {
					text = vformat("%d", tile_data->get_terrain_set());
				} else {
					text = "-";
				}
				Vector2 string_size = font->get_string_size(text, HORIZONTAL_ALIGNMENT_LEFT, -1, font_size);
				p_canvas_item->draw_string_outline(font, p_transform.xform(position) + Vector2i(-string_size.x / 2, string_size.y / 2), text, HORIZONTAL_ALIGNMENT_CENTER, string_size.x, font_size, 1, Color(0, 0, 0, 1));
				p_canvas_item->draw_string(font, p_transform.xform(position) + Vector2i(-string_size.x / 2, string_size.y / 2), text, HORIZONTAL_ALIGNMENT_CENTER, string_size.x, font_size, color);
			}
		}
	}
	p_canvas_item->draw_set_transform_matrix(Transform2D());
	if (drag_type == DRAG_TYPE_PAINT_TERRAIN_SET_RECT) {