### 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)

for (const KeyValue<Vector2i, TileMapQuadrant> &E : quadrant_map) {
		for (const RID &ci : E.value.canvas_items) {
			RenderingServer::get_singleton()->canvas_item_set_light_mask(ci, tile_map_node->get_light_mask());
		}
	}
	_rendering_update();
}
void TileMapLayer::notify_material_changed() {
	for (KeyValue<Vector2i, TileMapQuadrant> &E : quadrant_map) {
		TileMapQuadrant &q = E.value;
		for (const RID &ci : q.canvas_items) {
			RS::get_singleton()->canvas_item_set_use_parent_material(ci, tile_map_node->get_use_parent_material() || tile_map_node->get_material().is_valid());
		}
	}
	_rendering_update();
}
void TileMapLayer::notify_use_parent_material_changed() {
	notify_material_changed();
}
void TileMapLayer::notify_texture_filter_changed() {
	for (HashMap<Vector2i, TileMapQuadrant>::Iterator F = quadrant_map.begin(); F; ++F) {
		TileMapQuadrant &q = F->value;
		for (const RID &ci : q.canvas_items) {
			RenderingServer::get_singleton()->canvas_item_set_default_texture_filter(ci, RS::CanvasItemTextureFilter(tile_map_node->get_texture_filter_in_tree()));
			_make_quadrant_dirty(F);
		}
	}
	_rendering_update();
}
void TileMapLayer::notify_texture_repeat_changed() {