### 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 (!tile_map.has(p_coords)) {
		return TileMapCell();
	} else {
		TileMapCell c = tile_map.find(p_coords)->value;
		const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
		if (p_use_proxies && tile_set.is_valid()) {
			Array proxyed = tile_set->map_tile_proxy(c.source_id, c.get_atlas_coords(), c.alternative_tile);
			c.source_id = proxyed[0];
			c.set_atlas_coords(proxyed[1]);
			c.alternative_tile = proxyed[2];
		}
		return c;
	}
}
int TileMapLayer::get_effective_quadrant_size() const {
	
	if (tile_map_node->is_y_sort_enabled() && is_y_sort_enabled()) {
		return 1;
	} else {
		return tile_map_node->get_quadrant_size();
	}
}
void TileMapLayer::set_tile_data(TileMapLayer::DataFormat p_format, const Vector<int> &p_data) {