### 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)

#ifndef DISABLE_DEPRECATED
	ClassDB::bind_method(D_METHOD("set_navigation_map", "layer", "map"), &TileMap::set_layer_navigation_map);
	ClassDB::bind_method(D_METHOD("get_navigation_map", "layer"), &TileMap::get_layer_navigation_map);
#endif 
	ClassDB::bind_method(D_METHOD("set_collision_animatable", "enabled"), &TileMap::set_collision_animatable);
	ClassDB::bind_method(D_METHOD("is_collision_animatable"), &TileMap::is_collision_animatable);
	ClassDB::bind_method(D_METHOD("set_collision_visibility_mode", "collision_visibility_mode"), &TileMap::set_collision_visibility_mode);
	ClassDB::bind_method(D_METHOD("get_collision_visibility_mode"), &TileMap::get_collision_visibility_mode);
	ClassDB::bind_method(D_METHOD("set_navigation_visibility_mode", "navigation_visibility_mode"), &TileMap::set_navigation_visibility_mode);
	ClassDB::bind_method(D_METHOD("get_navigation_visibility_mode"), &TileMap::get_navigation_visibility_mode);
	ClassDB::bind_method(D_METHOD("set_cell", "layer", "coords", "source_id", "atlas_coords", "alternative_tile"), &TileMap::set_cell, DEFVAL(TileSet::INVALID_SOURCE), DEFVAL(TileSetSource::INVALID_ATLAS_COORDS), DEFVAL(0));
	ClassDB::bind_method(D_METHOD("erase_cell", "layer", "coords"), &TileMap::erase_cell);
	ClassDB::bind_method(D_METHOD("get_cell_source_id", "layer", "coords", "use_proxies"), &TileMap::get_cell_source_id, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_atlas_coords", "layer", "coords", "use_proxies"), &TileMap::get_cell_atlas_coords, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_alternative_tile", "layer", "coords", "use_proxies"), &TileMap::get_cell_alternative_tile, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_cell_tile_data", "layer", "coords", "use_proxies"), &TileMap::get_cell_tile_data, DEFVAL(false));
	ClassDB::bind_method(D_METHOD("get_coords_for_body_rid", "body"), &TileMap::get_coords_for_body_rid);
	ClassDB::bind_method(D_METHOD("get_layer_for_body_rid", "body"), &TileMap::get_layer_for_body_rid);
	ClassDB::bind_method(D_METHOD("get_pattern", "layer", "coords_array"), &TileMap::get_pattern);
	ClassDB::bind_method(D_METHOD("map_pattern", "position_in_tilemap", "coords_in_pattern", "pattern"), &TileMap::map_pattern);
	ClassDB::bind_method(D_METHOD("set_pattern", "layer", "position", "pattern"), &TileMap::set_pattern);
	ClassDB::bind_method(D_METHOD("set_cells_terrain_connect", "layer", "cells", "terrain_set", "terrain", "ignore_empty_terrains"), &TileMap::set_cells_terrain_connect, DEFVAL(true));
	ClassDB::bind_method(D_METHOD("set_cells_terrain_path", "layer", "path", "terrain_set", "terrain", "ignore_empty_terrains"), &TileMap::set_cells_terrain_path, DEFVAL(true));
	ClassDB::bind_method(D_METHOD("fix_invalid_tiles"), &TileMap::fix_invalid_tiles);
	ClassDB::bind_method(D_METHOD("clear_layer", "layer"), &TileMap::clear_layer);
	ClassDB::bind_method(D_METHOD("clear"), &TileMap::clear);
	ClassDB::bind_method(D_METHOD("force_update", "layer"), &TileMap::force_update, DEFVAL(-1));
	ClassDB::bind_method(D_METHOD("get_surrounding_cells", "coords"), &TileMap::get_surrounding_cells);
	ClassDB::bind_method(D_METHOD("get_used_cells", "layer"), &TileMap::get_used_cells);
	ClassDB::bind_method(D_METHOD("get_used_cells_by_id", "layer", "source_id", "atlas_coords", "alternative_tile"), &TileMap::get_used_cells_by_id, DEFVAL(TileSet::INVALID_SOURCE), DEFVAL(TileSetSource::INVALID_ATLAS_COORDS), DEFVAL(TileSetSource::INVALID_TILE_ALTERNATIVE));