Back then it would have been slightly tighter rules on hydrocarbons and NOX emissions. The $99 option probably got you a slightly different chip calibration with higher EGR duty cycles to pull the NOX down some more.
Or it may have just been a way for GM to take 99 extra dollars from you. If you still have the original chip, you could ask somebody like Eric Marshall to read it and see if it had any differences from a regular stock chip.