### 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)

int16_t x = decode_uint16(&local[0]);
		int16_t y = decode_uint16(&local[2]);
		if (p_format == TileMapLayer::FORMAT_3) {
			uint16_t source_id = decode_uint16(&local[4]);
			uint16_t atlas_coords_x = decode_uint16(&local[6]);
			uint16_t atlas_coords_y = decode_uint16(&local[8]);
			uint16_t alternative_tile = decode_uint16(&local[10]);
			set_cell(Vector2i(x, y), source_id, Vector2i(atlas_coords_x, atlas_coords_y), alternative_tile);
		} else {
#ifndef DISABLE_DEPRECATED
			
			uint32_t v = decode_uint32(&local[4]);
			
			bool flip_h = v & (1UL << 29);
			bool flip_v = v & (1UL << 30);
			bool transpose = v & (1UL << 31);
			v &= (1UL << 29) - 1;
			
			int16_t coord_x = 0;
			int16_t coord_y = 0;
			if (p_format == TileMapLayer::FORMAT_2) {
				coord_x = decode_uint16(&local[8]);
				coord_y = decode_uint16(&local[10]);
			}
			const Ref<TileSet> &tile_set = tile_map_node->get_tileset();
			if (tile_set.is_valid()) {
				Array a = tile_set->compatibility_tilemap_map(v, Vector2i(coord_x, coord_y), flip_h, flip_v, transpose);
				if (a.size() == 3) {
					set_cell(Vector2i(x, y), a[0], a[1], a[2]);
				} else {