### 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)

ERR_FAIL_COND(p_format > TileMapLayer::FORMAT_3);
	
	int c = p_data.size();
	const int *r = p_data.ptr();
	int offset = (p_format >= TileMapLayer::FORMAT_2) ? 3 : 2;
	ERR_FAIL_COND_MSG(c % offset != 0, vformat("Corrupted tile data. Got size: %s. Expected modulo: %s", offset));
	clear();
#ifdef DISABLE_DEPRECATED
	ERR_FAIL_COND_MSG(p_format != TileMapLayer::FORMAT_3, vformat("Cannot handle deprecated TileMap data format version %d. This Godot version was compiled with no support for deprecated data.", p_format));
#endif
	for (int i = 0; i < c; i += offset) {
		const uint8_t *ptr = (const uint8_t *)&r[i];
		uint8_t local[12];
		for (int j = 0; j < ((p_format >= TileMapLayer::FORMAT_2) ? 12 : 8); j++) {
			local[j] = ptr[j];
		}
#ifdef BIG_ENDIAN_ENABLED
		SWAP(local[0], local[3]);
		SWAP(local[1], local[2]);
		SWAP(local[4], local[7]);
		SWAP(local[5], local[6]);
		
		if (FORMAT >= FORMAT_2) {
			SWAP(local[8], local[11]);
			SWAP(local[9], local[10]);
		}
#endif