### 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.is_valid()) {
		return;
	}
	
	Vector2i tile_size = tile_set->get_tile_size();
	Vector<Vector2> polygon = tile_set->get_tile_shape_polygon();
	TileSet::TileShape shape = tile_set->get_tile_shape();
	for (const Vector2i &E : p_cells) {
		Vector2 center = map_to_local(E);
#define DRAW_SIDE_IF_NEEDED(side, polygon_index_from, polygon_index_to)                     \
	if (!p_cells.has(get_neighbor_cell(E, side))) {                                         \
		Vector2 from = p_transform.xform(center + polygon[polygon_index_from] * tile_size); \
		Vector2 to = p_transform.xform(center + polygon[polygon_index_to] * tile_size);     \
		p_control->draw_line(from, to, p_color);                                            \
	}
		if (shape == TileSet::TILE_SHAPE_SQUARE) {
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_RIGHT_SIDE, 1, 2);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_SIDE, 2, 3);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_LEFT_SIDE, 3, 0);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_SIDE, 0, 1);
		} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 2, 3);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE, 1, 2);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE, 0, 1);
			DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE, 3, 0);
		} else {
			if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
				DRAW_SIDE_IF_NEEDED(TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE, 3, 4);