Its all about the aerodynamics; the fluid Challenger body lines along the rear quarter, combined with the sweeping curve at the top of the quarter window promote smoother movement through the air at speed. The simpler body line and that angled break on the Barracuda window promote more turbulence, impacting performance and fuel economy.
Well, Chrysler had already poured their styling and aero-engineering all into the Challenger, and the only way to fix it would be to make the Barracuda look more like the Challenger, and that kind of defeats the purpose of having two car lines, so in order to make sure the Barracuda, comparably equipped re: drivetrain, could at _least_ travel as far as the Challenger on a full tank of gas, it got a bigger tank.
Or so I heard ; )