### 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)

if (cell.source_id != TileSet::INVALID_SOURCE) {
				Ref<TileSetSource> source = tile_set->get_source(cell.source_id);
				Ref<TileSetAtlasSource> atlas_source = source;
				if (atlas_source.is_valid()) {
					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 && tile_data->get_terrain() == p_terrain) {
				connect = true;
			}
		}
		if (connect) {
			cells_with_terrain_center_bit.insert(coords);
		}
	}
	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 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)) {
				c = TerrainConstraint(tile_map_node, coords, bit, p_terrain);
				c.set_priority(10);
				if ((int(bit) % 2) == 0) {