### 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)

TerrainConstraint terrain_bit_constraint = TerrainConstraint(tile_map_node, p_position, bit, terrain_pattern.get_terrain_peering_bit(bit));
				in_set_constraint_element = p_constraints.find(terrain_bit_constraint);
				if (in_set_constraint_element) {
					if (in_set_constraint_element->get().get_terrain() != terrain_bit_constraint.get_terrain()) {
						score += in_set_constraint_element->get().get_priority();
					}
				} else if (p_current_pattern.get_terrain_peering_bit(bit) != terrain_pattern.get_terrain_peering_bit(bit)) {
					invalid_pattern = true; 
					break;
				}
			}
		}
		if (invalid_pattern) {
			continue;
		}
		terrain_pattern_score[terrain_pattern] = score;
	}
	
	TileSet::TerrainsPattern min_score_pattern = p_current_pattern;
	int min_score = INT32_MAX;
	for (KeyValue<TileSet::TerrainsPattern, int> E : terrain_pattern_score) {
		if (E.value < min_score) {
			min_score_pattern = E.key;
			min_score = E.value;
		}
	}
	return min_score_pattern;
}
RBSet<TerrainConstraint> TileMapLayer::_get_terrain_constraints_from_added_pattern(const Vector2i &p_position, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern) const {