### 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)

return bodies_coords.has(p_physics_body);
}
Vector2i TileMapLayer::get_coords_for_body_rid(RID p_physics_body) const {
	return bodies_coords[p_physics_body];
}
HashMap<Vector2i, TileSet::CellNeighbor> TerrainConstraint::get_overlapping_coords_and_peering_bits() const {
	HashMap<Vector2i, TileSet::CellNeighbor> output;
	ERR_FAIL_COND_V(is_center_bit(), output);
	Ref<TileSet> ts = tile_map->get_tileset();
	ERR_FAIL_COND_V(!ts.is_valid(), output);
	TileSet::TileShape shape = ts->get_tile_shape();
	if (shape == TileSet::TILE_SHAPE_SQUARE) {
		switch (bit) {
			case 1:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_RIGHT_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_LEFT_SIDE;
				break;
			case 2:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_RIGHT_SIDE)] = TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_CORNER)] = TileSet::CELL_NEIGHBOR_TOP_LEFT_CORNER;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_RIGHT_CORNER;
				break;
			case 3:
				output[base_cell_coords] = TileSet::CELL_NEIGHBOR_BOTTOM_SIDE;
				output[tile_map->get_neighbor_cell(base_cell_coords, TileSet::CELL_NEIGHBOR_BOTTOM_SIDE)] = TileSet::CELL_NEIGHBOR_TOP_SIDE;
				break;
			default:
				ERR_FAIL_V(output);