### 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)

base_cell_coords = p_position;
				break;
			case TileSet::CELL_NEIGHBOR_LEFT_CORNER:
				bit = 2;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE:
				bit = 1;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_LEFT_SIDE);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_CORNER:
				bit = 2;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_CORNER);
				break;
			case TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE:
				bit = 3;
				base_cell_coords = p_tile_map->get_neighbor_cell(p_position, TileSet::CELL_NEIGHBOR_TOP_RIGHT_SIDE);
				break;
			default:
				ERR_FAIL();
				break;
		}
	} else {
		
		TileSet::TileOffsetAxis offset_axis = ts->get_tile_offset_axis();
		if (offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			switch (p_bit) {
				case TileSet::CELL_NEIGHBOR_RIGHT_SIDE:
					bit = 1;
					base_cell_coords = p_position;