### 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 (max > 0) {
			TerrainConstraint c = E_constraint;
			c.set_terrain(max_terrain);
			constraints.insert(c);
		}
	}
	
	for (Vector2i E_coords : p_painted) {
		TileData *tile_data = nullptr;
		TileMapCell cell = get_cell(E_coords);
		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);
			}
		}
		int terrain = (tile_data && tile_data->get_terrain_set() == p_terrain_set) ? tile_data->get_terrain() : -1;
		if (!p_ignore_empty_terrains || terrain >= 0) {
			constraints.insert(TerrainConstraint(tile_map_node, E_coords, terrain));
		}
	}
	return constraints;
}
void TileMapLayer::set_tile_map(TileMap *p_tile_map) {
	tile_map_node = p_tile_map;
}
void TileMapLayer::set_layer_index_in_tile_map_node(int p_index) {