### 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)

if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x -= 1;
					if (coords_in_pattern.x < 0) {
						ensure_positive_offset.x = 1;
					}
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y -= 1;
					if (coords_in_pattern.y < 0) {
						ensure_positive_offset.y = 1;
					}
				}
			} else if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED_OFFSET) {
				if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(min.y % 2) && bool(coords_in_pattern.y % 2)) {
					coords_in_pattern.x += 1;
				} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(min.x % 2) && bool(coords_in_pattern.x % 2)) {
					coords_in_pattern.y += 1;
				}
			}
		}
		coords_in_pattern_array.write[i] = coords_in_pattern;
	}
	for (int i = 0; i < coords_in_pattern_array.size(); i++) {
		Vector2i coords = p_coords_array[i];
		Vector2i coords_in_pattern = coords_in_pattern_array[i];
		output->set_cell(coords_in_pattern + ensure_positive_offset, get_cell_source_id(coords), get_cell_atlas_coords(coords), get_cell_alternative_tile(coords));
	}
	return output;
}
void TileMapLayer::set_pattern(const Vector2i &p_position, const Ref<TileMapPattern> p_pattern) {