### 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)

int16_t x = decode_uint16(&local[0]);
		int16_t y = decode_uint16(&local[2]);
		if (p_format == TileMapLayer::FORMAT_3) {
			uint16_t source_id = decode_uint16(&local[4]);
			uint16_t atlas_coords_x = decode_uint16(&local[6]);
			uint16_t atlas_coords_y = decode_uint16(&local[8]);
			uint16_t alternative_tile = decode_uint16(&local[10]);
			set_cell(Vector2i(x, y), source_id, Vector2i(atlas_coords_x, atlas_coords_y), alternative_tile);
		} else {
#ifndef DISABLE_DEPRECATED
			
			uint32_t v = decode_uint32(&local[4]);
			
			bool flip_h = v & (1UL << 29);
			bool flip_v = v & (1UL << 30);
			bool transpose = v & (1UL << 31);
			v &= (1UL << 29) - 1;
			
			int16_t coord_x = 0;
			int16_t coord_y = 0;
			if (p_format == TileMapLayer::FORMAT_2) {
				coord_x = decode_uint16(&local[8]);
				coord_y = decode_uint16(&local[10]);
			}
			const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
			if (tile_set.is_valid()) {
				Array a = tile_set->compatibility_tilemap_map(v, Vector2i(coord_x, coord_y), flip_h, flip_v, transpose);
				if (a.size() == 3) {
					set_cell(Vector2i(x, y), a[0], a[1], a[2]);
				} else {