### 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)

dest_rect.size = atlas_source->get_runtime_tile_texture_region(p_atlas_coords).size;
		dest_rect.size.x += FP_ADJUST;
		dest_rect.size.y += FP_ADJUST;
		bool transpose = tile_data->get_transpose();
		if (transpose) {
			dest_rect.position = (p_position - Vector2(dest_rect.size.y, dest_rect.size.x) / 2 - tile_offset);
		} else {
			dest_rect.position = (p_position - dest_rect.size / 2 - tile_offset);
		}
		if (tile_data->get_flip_h()) {
			dest_rect.size.x = -dest_rect.size.x;
		}
		if (tile_data->get_flip_v()) {
			dest_rect.size.y = -dest_rect.size.y;
		}
		
		if (p_frame >= 0) {
			Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, p_frame);
			tex->draw_rect_region(p_canvas_item, dest_rect, source_rect, modulate, transpose, p_tile_set->is_uv_clipping());
		} else if (atlas_source->get_tile_animation_frames_count(p_atlas_coords) == 1) {
			Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, 0);
			tex->draw_rect_region(p_canvas_item, dest_rect, source_rect, modulate, transpose, p_tile_set->is_uv_clipping());
		} else {
			real_t speed = atlas_source->get_tile_animation_speed(p_atlas_coords);
			real_t animation_duration = atlas_source->get_tile_animation_total_duration(p_atlas_coords) / speed;
			real_t time = 0.0;
			for (int frame = 0; frame < atlas_source->get_tile_animation_frames_count(p_atlas_coords); frame++) {
				real_t frame_duration = atlas_source->get_tile_animation_frame_duration(p_atlas_coords, frame) / speed;
				RenderingServer::get_singleton()->canvas_item_add_animation_slice(p_canvas_item, animation_duration, time, time + frame_duration, p_animation_offset);
				Rect2i source_rect = atlas_source->get_runtime_tile_texture_region(p_atlas_coords, frame);