### 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_FAIL_COND_MSG(!tile_map_node->is_inside_tree(), "A TileMap navigation map can only be changed while inside the SceneTree.");
	navigation_map = p_map;
	uses_world_navigation_map = p_map == tile_map_node->get_world_2d()->get_navigation_map();
}
RID TileMapLayer::get_navigation_map() const {
	if (navigation_map.is_valid()) {
		return navigation_map;
	}
	return RID();
}
void TileMapLayer::force_update() {
	clear_internals();
	recreate_internals();
}
void TileMapLayer::fix_invalid_tiles() {
	Ref<TileSet> tileset = tile_map_node->get_tileset();
	ERR_FAIL_COND_MSG(tileset.is_null(), "Cannot call fix_invalid_tiles() on a TileMap without a valid TileSet.");
	RBSet<Vector2i> coords;
	for (const KeyValue<Vector2i, TileMapCell> &E : tile_map) {
		TileSetSource *source = *tileset->get_source(E.value.source_id);
		if (!source || !source->has_tile(E.value.get_atlas_coords()) || !source->has_alternative_tile(E.value.get_atlas_coords(), E.value.alternative_tile)) {
			coords.insert(E.key);
		}
	}
	for (const Vector2i &E : coords) {
		set_cell(E, TileSet::INVALID_SOURCE, TileSetSource::INVALID_ATLAS_COORDS, TileSetSource::INVALID_TILE_ALTERNATIVE);
	}
}
bool TileMapLayer::has_body_rid(RID p_physics_body) const {