### 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)

CanvasItem::set_use_parent_material(p_use_parent_material);
	
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_use_parent_material_changed();
	}
}
void TileMap::set_texture_filter(TextureFilter p_texture_filter) {
	
	CanvasItem::set_texture_filter(p_texture_filter);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_texture_filter_changed();
	}
}
void TileMap::set_texture_repeat(CanvasItem::TextureRepeat p_texture_repeat) {
	
	CanvasItem::set_texture_repeat(p_texture_repeat);
	for (Ref<TileMapLayer> &layer : layers) {
		layer->notify_texture_repeat_changed();
	}
}
TypedArray<Vector2i> TileMap::get_surrounding_cells(const Vector2i &coords) {
	if (!tile_set.is_valid()) {
		return TypedArray<Vector2i>();
	}
	TypedArray<Vector2i> around;
	TileSet::TileShape shape = tile_set->get_tile_shape();