### 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)

TILEMAP_CALL_FOR_LAYER_V(p_layer, TypedArray<Vector2i>(), get_used_cells_by_id);
}
Rect2i TileMap::get_used_rect() const {
	
	if (layers.is_empty()) {
		return Rect2i();
	}
	Rect2 rect = layers[0]->get_used_rect();
	for (unsigned int i = 1; i < layers.size(); i++) {
		rect = rect.merge(layers[i]->get_used_rect());
	}
	return rect;
}
void TileMap::set_light_mask(int p_light_mask) {
	
	CanvasItem::set_light_mask(p_light_mask);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_light_mask_changed();
	}
}
void TileMap::set_material(const Ref<Material> &p_material) {
	
	CanvasItem::set_material(p_material);
	
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_material_changed();
	}
}
void TileMap::set_use_parent_material(bool p_use_parent_material) {