### 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)

layer_index_in_tile_map_node = p_index;
}
Rect2 TileMapLayer::get_rect(bool &r_changed) const {
	
	r_changed = false;
#ifdef DEBUG_ENABLED
	if (rect_cache_dirty) {
		Rect2 r_total;
		bool first = true;
		for (const KeyValue<Vector2i, TileMapQuadrant> &E : quadrant_map) {
			Rect2 r;
			r.position = tile_map_node->map_to_local(E.key * get_effective_quadrant_size());
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(1, 0)) * get_effective_quadrant_size()));
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(1, 1)) * get_effective_quadrant_size()));
			r.expand_to(tile_map_node->map_to_local((E.key + Vector2i(0, 1)) * get_effective_quadrant_size()));
			if (first) {
				r_total = r;
				first = false;
			} else {
				r_total = r_total.merge(r);
			}
		}
		r_changed = rect_cache != r_total;
		rect_cache = r_total;
		rect_cache_dirty = false;
	}
#endif
	return rect_cache;
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMapLayer::terrain_fill_constraints(const Vector<Vector2i> &p_to_replace, int p_terrain_set, const RBSet<TerrainConstraint> &p_constraints) {