Unless it was some kind of emergency, it would be extremely unlikely that a train op would take a Physical Needs Relief (PNR) on a running line at a random station where they would have to be escorted to the toilet - that has the potential to be extremely detrimental to the service. I certainly know where all my PNR points are on my line - at termini, occasional head walls, and other secret doors
IIRC, Rule Book 6 states "must" tell the controller, but agree that it seems to have fallen by the wayside a little these days.