### 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)

TileSet::CellNeighbor bit = TileSet::CellNeighbor(j);
			if (tile_set->is_valid_terrain_peering_bit(p_terrain_set, bit)) {
				Vector2i neighbor = tile_map_node->get_neighbor_cell(coords, bit);
				if (!can_modify_set.has(neighbor)) {
					can_modify_list.push_back(neighbor);
					can_modify_set.insert(neighbor);
				}
			}
		}
	}
	
	RBSet<TerrainConstraint> constraints;
	
	for (Vector2i coords : p_coords_array) {
		
		RBSet<TerrainConstraint> added_constraints = _get_terrain_constraints_from_added_pattern(coords, p_terrain_set, p_terrains_pattern);
		for (TerrainConstraint c : added_constraints) {
			c.set_priority(10);
			constraints.insert(c);
		}
	}
	
	for (TerrainConstraint c : _get_terrain_constraints_from_painted_cells_list(painted_set, p_terrain_set, p_ignore_empty_terrains)) {
		constraints.insert(c);
	}
	
	output = terrain_fill_constraints(can_modify_list, p_terrain_set, constraints);
	return output;
}
TileMapCell TileMapLayer::get_cell(const Vector2i &p_coords, bool p_use_proxies) const {