Using the flight time compensation option was the only correct method to calculate flight time for bus timing analysis. It was added as an option long ago because the very early versions of HyperLynx SI did not use flight time compensation. After having the method be optional for some years to allow users time to adjust to the correct method, the batch simulation wizard simply dropped the old, incorrect method. Starting HyperLynx SI VX.2.3 the flight times are always reported as compensated flight times given that the driving IBIS model includes a valid timing reference load (Vmeas, Vref, Rref, Cref).
Note that it is important that the timing reference load in the IBIS driver match the reference load used to measure the IC propagation delays specified in the IC datasheet.