### Godot version

4.2.dev3.official[013e8e3af]

### System information

Godot v4.2.dev3 - Arch Linux #1 SMP PREEMPT_DYNAMIC Fri, 11 Aug 2023 11:03:36 +0000 - X11 - GLES3 (Compatibility) - NVIDIA GeForce RTX 2060 (nvidia; 535.98) - Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz (16 Threads)

### Issue description

`TileMap.get_used_cells_by_id()` seems not work as expected.
It seems that this method will return the same result as "TileMap.get_used_cells()" since Godot 4.2dev2.
The arguments  (`source_id: int`, `atlas_coords: Vector2i`, `alternative_tile: int`) of `get_used_cells_by_id()` seems not make the filter working as expected.  It would only return the same result as `get_used_cells()`, contains all the tiles on the layer.

### Steps to reproduce

1. create a tilemap scene
2. attach a tileset, that contains  at least 2 tiles , paint some tiles.
3. calls Tilemap.get_used_cells_by_id(layer, source_id, atlas_coords,alternative_tile)
4. run it

### Minimal reproduction project

run tile_map.tscn by Godot4dev3 (or custom build)
[tilemap_debug.zip](https://github.com/godotengine/godot/files/12369631/tilemap_debug.zip)

ERR_FAIL_COND(!tile_map_node->is_inside_tree());
	const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
	ERR_FAIL_COND(!tile_set.is_valid());
	Transform2D tilemap_xform = tile_map_node->get_global_transform();
	SelfList<TileMapQuadrant> *q_list_element = r_dirty_quadrant_list.first();
	while (q_list_element) {
		TileMapQuadrant &q = *q_list_element->self();
		
		for (const KeyValue<Vector2i, Vector<RID>> &E : q.navigation_regions) {
			for (int i = 0; i < E.value.size(); i++) {
				RID region = E.value[i];
				if (!region.is_valid()) {
					continue;
				}
				NavigationServer2D::get_singleton()->region_set_map(region, RID());
			}
		}
		q.navigation_regions.clear();
		
		for (const Vector2i &E_cell : q.cells) {
			TileMapCell c = get_cell(E_cell, true);
			TileSetSource *source;
			if (tile_set->has_source(c.source_id)) {
				source = *tile_set->get_source(c.source_id);
				if (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
					continue;
				}
				TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);