### 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)

const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	if (!tile_set.is_valid()) {
		return RBSet<TerrainConstraint>();
	}
	ERR_FAIL_INDEX_V(p_terrain_set, tile_set->get_terrain_sets_count(), RBSet<TerrainConstraint>());
	
	RBSet<TerrainConstraint> dummy_constraints;
	for (const Vector2i &E : p_painted) {
		for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) { 
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				dummy_constraints.insert(TerrainConstraint(tile_map_node, E, bit, -1));
			}
		}
	}
	
	RBSet<TerrainConstraint> constraints;
	for (const TerrainConstraint &E_constraint : dummy_constraints) {
		HashMap<int, int> terrain_count;