### 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)

TileData *tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
				if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
					current_pattern = tile_data->get_terrains_pattern();
				}
			}
		}
		TileSet::TerrainsPattern pattern = _get_best_terrain_pattern_for_constraints(p_terrain_set, coords, constraints, current_pattern);
		
		RBSet<TerrainConstraint> new_constraints = _get_terrain_constraints_from_added_pattern(coords, p_terrain_set, pattern);
		for (const TerrainConstraint &E_constraint : new_constraints) {
			if (constraints.has(E_constraint)) {
				constraints.erase(E_constraint);
			}
			TerrainConstraint c = E_constraint;
			c.set_priority(5);
			constraints.insert(c);
		}
		output[coords] = pattern;
	}
	return output;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_connect(const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> output;
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND_V(!tile_set.is_valid(), output);
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), output);
	
	Vector<Vector2i> can_modify_list;
	RBSet<Vector2i> can_modify_set;