### 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 (max > 0) {
			TerrainConstraint c = E_constraint;
			c.set_terrain(max_terrain);
			constraints.insert(c);
		}
	}
	
	for (Vector2i E_coords : p_painted) {
		TileData *tile_data = nullptr;
		TileMapCell cell = get_cell(E_coords);
		if (cell.source_id != TileSet::INVALID_SOURCE) {
			Ref<TileSetSource> source = tile_set->get_source(cell.source_id);
			Ref<TileSetAtlasSource> atlas_source = source;
			if (atlas_source.is_valid()) {
				tile_data = atlas_source->get_tile_data(cell.get_atlas_coords(), cell.alternative_tile);
			}
		}
		int terrain = (tile_data && tile_data->get_terrain_set() == p_terrain_set) ? tile_data->get_terrain() : -1;
		if (!p_ignore_empty_terrains || terrain >= 0) {
			constraints.insert(TerrainConstraint(tile_map_node, E_coords, terrain));
		}
	}
	return constraints;
}
void TileMapLayer::set_tile_map(TileMap *p_tile_map) {
	tile_map_node = p_tile_map;
}
void TileMapLayer::set_layer_index_in_tile_map_node(int p_index) {