### 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)

ret += Vector2i(-1, Math::posmod(Math::floor(ret.x), 2) ? 1 : 0);
					}
					break;
				case TileSet::TILE_LAYOUT_STACKED_OFFSET:
					ret = ret.floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, Math::posmod(Math::floor(ret.x), 2) ? -1 : 0);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(-1, Math::posmod(Math::floor(ret.x), 2) ? 0 : 1);
					}
					break;
				case TileSet::TILE_LAYOUT_STAIRS_RIGHT:
					ret = Vector2(ret.x / 2 - ret.y, ret.y * 2).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(0, -1);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(-1, 1);
					}
					break;
				case TileSet::TILE_LAYOUT_STAIRS_DOWN:
					ret = Vector2(ret.x, ret.y - ret.x / 2).floor();
					if (in_top_left_triangle) {
						ret += Vector2i(-1, 0);
					} else if (in_bottom_left_triangle) {
						ret += Vector2i(-1, 1);
					}
					break;
				case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
					ret = Vector2(ret.x / 2 - ret.y, ret.y + ret.x / 2).floor();
					if (in_top_left_triangle) {