This is also wrong. The actual proposals for MNT involve creating a system that is very stable, so you can measure it safely. The actual machinery is a bunch of parts that are as strong as they can possibly be made (this is why the usual proposals involve covalent bonded carbon aka diamond) so they are stable and you can poke them with a probe. You keep the box as cold as practical.

It's true that even if you set everything up perfectly, there are some events that can't be observed directly, such as bonding and rearrangements that could destroy the machine. In addition, practical MNT systems would be 3d mazes of machinery stacked on top of each other, so it would be very difficult to diagnose failures. To summarize : in a world with working MNT, there's still lots of work that has to be done.