### 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)

HashMap<Vector2i, TileSet::CellNeighbor> overlapping_terrain_bits = E_constraint.get_overlapping_coords_and_peering_bits();
		for (const KeyValue<Vector2i, TileSet::CellNeighbor> &E_overlapping : overlapping_terrain_bits) {
			TileData *neighbor_tile_data = nullptr;
			TileMapCell neighbor_cell = get_cell(E_overlapping.key);
			if (neighbor_cell.source_id != TileSet::INVALID_SOURCE) {
				Ref<TileSetSource> source = tile_set->get_source(neighbor_cell.source_id);
				Ref<TileSetAtlasSource> atlas_source = source;
				if (atlas_source.is_valid()) {
					TileData *tile_data = atlas_source->get_tile_data(neighbor_cell.get_atlas_coords(), neighbor_cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						neighbor_tile_data = tile_data;
					}
				}
			}
			int terrain = neighbor_tile_data ? neighbor_tile_data->get_terrain_peering_bit(TileSet::CellNeighbor(E_overlapping.value)) : -1;
			if (!p_ignore_empty_terrains || terrain >= 0) {
				if (!terrain_count.has(terrain)) {
					terrain_count[terrain] = 0;
				}
				terrain_count[terrain] += 1;
			}
		}
		
		int max = 0;
		int max_terrain = -1;
		for (const KeyValue<int, int> &E_terrain_count : terrain_count) {
			if (E_terrain_count.value > max) {
				max = E_terrain_count.value;
				max_terrain = E_terrain_count.key;
			}