### 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 (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
				continue;
			}
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				Vector2i grid_size = atlas_source->get_atlas_grid_size();
				if (!atlas_source->get_runtime_texture().is_valid() || c.get_atlas_coords().x >= grid_size.x || c.get_atlas_coords().y >= grid_size.y) {
					
					Array to_hash;
					to_hash.push_back(c.source_id);
					to_hash.push_back(c.get_atlas_coords());
					to_hash.push_back(c.alternative_tile);
					uint32_t hash = RandomPCG(to_hash.hash()).rand();
					Color color;
					color = color.from_hsv(
							(float)((hash >> 24) & 0xFF) / 256.0,
							Math::lerp(0.5, 1.0, (float)((hash >> 16) & 0xFF) / 256.0),
							Math::lerp(0.5, 1.0, (float)((hash >> 8) & 0xFF) / 256.0),
							0.8);
					
					Transform2D cell_to_quadrant;
					cell_to_quadrant.set_origin(tile_map_node->map_to_local(E_cell) - quadrant_pos);
					rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, cell_to_quadrant);
					rs->canvas_item_add_circle(p_quadrant->debug_canvas_item, Vector2(), MIN(tile_set->get_tile_size().x, tile_set->get_tile_size().y) / 4.0, color);
				}
			}
		}
	}
}
void TileMapLayer::_physics_update_dirty_quadrants(SelfList<TileMapQuadrant>::List &r_dirty_quadrant_list) {