### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

ERR_PRINT(vformat("No valid tile in Tileset for: tile:%s coords:%s flip_h:%s flip_v:%s transpose:%s", v, Vector2i(coord_x, coord_y), flip_h, flip_v, transpose));
				}
			} else {
				int compatibility_alternative_tile = ((int)flip_h) + ((int)flip_v << 1) + ((int)transpose << 2);
				set_cell(Vector2i(x, y), v, Vector2i(coord_x, coord_y), compatibility_alternative_tile);
			}
#endif
		}
	}
}
Vector<int> TileMapLayer::get_tile_data() const {
	
	Vector<int> tile_data;
	tile_data.resize(tile_map.size() * 3);
	int *w = tile_data.ptrw();
	
	int idx = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		uint8_t *ptr = (uint8_t *)&w[idx];
		encode_uint16((int16_t)(E.key.x), &ptr[0]);
		encode_uint16((int16_t)(E.key.y), &ptr[2]);
		encode_uint16(E.value.source_id, &ptr[4]);
		encode_uint16(E.value.coord_x, &ptr[6]);
		encode_uint16(E.value.coord_y, &ptr[8]);
		encode_uint16(E.value.alternative_tile, &ptr[10]);
		idx += 3;
	}
	return tile_data;
}
void TileMapLayer::clear_instantiated_scenes() {