### 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)

}
	} else if (shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		switch (bit) {
			case 1:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE;
				break;
			case 2:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_CORNER)] = TileSet::CELL_NEIGHBOR_TOP_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE)] = TileSet::CELL_NEIGHBOR_RIGHT_CORNER;
				break;
			case 3:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE;
				break;
			default:
				ERR_FAIL_V(output);
		}
	} else {
		
		TileSet::TileOffsetAxis offset_axis = ts->get_tile_offset_axis();
		if (offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			switch (bit) {
				case 1:
					output[base_cell_coords] = TileSet::CELL_NEIGHBOR_RIGHT_SIDE;
					output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_SIDE;
					break;
				case 2: