### 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)

ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	if (navigation_map.is_valid()) {
		if (uses_world_navigation_map) {
			
			return;
		}
		NavigationServer2D::get_singleton()->free(navigation_map);
		navigation_map = RID();
	}
}
void TileMapLayer::_navigation_cleanup_quadrant(TileMapQuadrant *p_quadrant) {
	
	ERR_FAIL_NULL(NavigationServer2D::get_singleton());
	for (const KeyValue<Vector2i, Vector<RID>> &E : p_quadrant->navigation_regions) {
		for (int i = 0; i < E.value.size(); i++) {
			RID region = E.value[i];
			if (!region.is_valid()) {
				continue;
			}
			NavigationServer2D::get_singleton()->free(region);
		}
	}
	p_quadrant->navigation_regions.clear();
}
void TileMapLayer::_navigation_draw_quadrant_debug(TileMapQuadrant *p_quadrant) {