### 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)
if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x -= 1;
					if (coords_in_pattern.x < 0) {
						ensure_positive_offset.x = 1;
					}
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y -= 1;
					if (coords_in_pattern.y < 0) {
						ensure_positive_offset.y = 1;
					}
				}
			} else if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED_OFFSET) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x += 1;
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y += 1;
				}
			}
		}
		coords_in_pattern_array.write[i] = coords_in_pattern;
	}
	for (int i = 0; i < coords_in_pattern_array.size(); i++) {
		Vector2i coords = p_coords_array[i];
		Vector2i coords_in_pattern = coords_in_pattern_array[i];
		output->set_cell(coords_in_pattern + ensure_positive_offset, get_cell_source_id(coords), get_cell_atlas_coords(coords), get_cell_alternative_tile(coords));
	}
	return output;
}
void TileMapLayer::set_pattern(const Vector2i &p_position, const Ref<TileMapPattern> p_pattern) {