### 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 ((p_from_layout == TileSet::TILE_LAYOUT_STAIRS_RIGHT) ^ (p_offset_axis == TileSet::TILE_OFFSET_AXIS_VERTICAL)) {
				if (output.y < 0 && bool(output.y % 2)) {
					output = Vector2i(output.x + output.y / 2 - 1, output.y);
				} else {
					output = Vector2i(output.x + output.y / 2, output.y);
				}
			} else {
				if (output.x < 0 && bool(output.x % 2)) {
					output = Vector2i(output.x / 2 - 1, output.x + output.y * 2);
				} else {
					output = Vector2i(output.x / 2, output.x + output.y * 2);
				}
			}
			break;
		case TileSet::TILE_LAYOUT_DIAMOND_RIGHT:
		case TileSet::TILE_LAYOUT_DIAMOND_DOWN:
			if ((p_from_layout == TileSet::TILE_LAYOUT_DIAMOND_RIGHT) ^ (p_offset_axis == TileSet::TILE_OFFSET_AXIS_VERTICAL)) {
				if ((output.x + output.y) < 0 && (output.x - output.y) % 2) {
					output = Vector2i((output.x + output.y) / 2 - 1, output.y - output.x);
				} else {
					output = Vector2i((output.x + output.y) / 2, -output.x + output.y);
				}
			} else {
				if ((output.x - output.y) < 0 && (output.x + output.y) % 2) {
					output = Vector2i((output.x - output.y) / 2 - 1, output.x + output.y);
				} else {
					output = Vector2i((output.x - output.y) / 2, output.x + output.y);
				}
			}
			break;