Solutions?
If the ATCo needs to use the restroom, it would be advisable to carry on a portable VHF transceiver and also inform the APP operator... in airports where the approach operator can see the runway, it would be simpler to deal with an "organic emergency". When you have to go you have to go!
The chance that anyone would enter an active runway without radio contact is in my opinion almost zero, (in a controlled airport) so I think misunderstandings are far more dangerous.
At least two operators should be available for the night shift, too.