Drag Supras are quicker with automatic transmissions because the automatic allows you to keep your foot on the throttle during shifts. These cars all have bigass turbos that fall off boost during a manual shift (which involves taking your foot off the gas) but an auto keeps the turbo spooled for the whole run.

A Supra set up for road racing or something like that would not have as monstrous of a turbo and thus would be quicker with a manual at its specified purpose.