Hello,
you don't need to take the train - you just have to make sure that the flight number isn't LX2990 or LX2991 - these aren't trains...
The answer you got from the Swiss helpline is pure BS (were you connected with Cape Town or Bombay?).
Who should check your presence on the train, and how should this be done?
As you can take every train the day the ticket is issued for, and board and deboard everywhere between Zurich Airport and Basle, there is a big chance anyway that no ticket controller sees your ticket.
BTW: Welcome to Flyertalk!