### 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)

RBSet<Vector2i> painted_set;
	for (int i = p_coords_array.size() - 1; i >= 0; i--) {
		const Vector2i &coords = p_coords_array[i];
		can_modify_list.push_back(coords);
		can_modify_set.insert(coords);
		painted_set.insert(coords);
	}
	for (Vector2i coords : p_coords_array) {
		
		for (int j = 0; j < TileSet::CELL_NEIGHBOR_MAX; j++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
				if (!can_modify_set.has(neighbor)) {
					can_modify_list.push_back(neighbor);
					can_modify_set.insert(neighbor);
				}
			}
		}
	}
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		TerrainConstraint c = TerrainConstraint(tile_map_node, coords, p_terrain);
		c.set_priority(10);
		constraints.insert(c);
	}
	for (int i = 0; i < p_coords_array.size() - 1; i++) {