### 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)

HashMap<Vector2i, TileSet::CellNeighbor> overlapping_terrain_bits = E_constraint.get_overlapping_coords_and_peering_bits();
		for (const KeyValue<Vector2i, TileSet::CellNeighbor> &E_overlapping : overlapping_terrain_bits) {
			TileData *neighbor_tile_data = nullptr;
			TileMapCell neighbor_cell = get_cell(E_overlapping.key);
			if (neighbor_cell.source_id != TileSet::INVALID_SOURCE) {
				Ref<TileSetSource> source = tile_set->get_source(neighbor_cell.source_id);
				Ref<TileSetAtlasSource> atlas_source = source;
				if (atlas_source.is_valid()) {
					TileData *tile_data = atlas_source->get_tile_data(neighbor_cell.get_atlas_coords(), neighbor_cell.alternative_tile);
					if (tile_data && tile_data->get_terrain_set() == p_terrain_set) {
						neighbor_tile_data = tile_data;
					}
				}
			}
			int terrain = neighbor_tile_data ? neighbor_tile_data->get_terrain_peering_bit(TileSet::CellNeighbor(E_overlapping.value)) : -1;
			if (!p_ignore_empty_terrains || terrain >= 0) {
				if (!terrain_count.has(terrain)) {
					terrain_count[terrain] = 0;
				}
				terrain_count[terrain] += 1;
			}
		}
		
		int max = 0;
		int max_terrain = -1;
		for (const KeyValue<int, int> &E_terrain_count : terrain_count) {
			if (E_terrain_count.value > max) {
				max = E_terrain_count.value;
				max_terrain = E_terrain_count.key;
			}