### 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)

_erase_quadrant(Q);
		} else {
			_make_quadrant_dirty(Q);
		}
		used_rect_cache_dirty = true;
	} else {
		if (!E) {
			
			E = tile_map.insert(pk, TileMapCell());
			
			if (!Q) {
				Q = _create_quadrant(qk);
			}
			TileMapQuadrant &q = Q->value;
			q.cells.insert(pk);
		} else {
			ERR_FAIL_COND(!Q); 
			if (E->value.source_id == source_id && E->value.get_atlas_coords() == atlas_coords && E->value.alternative_tile == alternative_tile) {
				return; 
			}
		}
		TileMapCell &c = E->value;
		c.source_id = source_id;
		c.set_atlas_coords(atlas_coords);
		c.alternative_tile = alternative_tile;
		_make_quadrant_dirty(Q);
		used_rect_cache_dirty = true;
	}
}
void TileMapLayer::erase_cell(const Vector2i &p_coords) {