### 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 (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x -= 1;
					if (coords_in_pattern.x < 0) {
						ensure_positive_offset.x = 1;
					}
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y -= 1;
					if (coords_in_pattern.y < 0) {
						ensure_positive_offset.y = 1;
					}
				}
			} else if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED_OFFSET) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x += 1;
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y += 1;
				}
			}
		}
		coords_in_pattern_array.write[i] = coords_in_pattern;
	}
	for (int i = 0; i < coords_in_pattern_array.size(); i++) {
		Vector2i coords = p_coords_array[i];
		Vector2i coords_in_pattern = coords_in_pattern_array[i];
		output->set_cell(coords_in_pattern + ensure_positive_offset, get_cell_source_id(coords), get_cell_atlas_coords(coords), get_cell_alternative_tile(coords));
	}
	return output;
}
void TileMapLayer::set_pattern(const Vector2i &p_position, const Ref<TileMapPattern> p_pattern) {