ok, put it this way, a stock auto will have a 1K TC and very low line pressure. A stock auto is a very lossy system thats made for comfort - how many racecars use OEM clutches and stock gearsets? Take a Chrysler 727 Torqueflite auto (as found in the likes of Aston Martins, Bristols, Jensens etc etc), add a performance drum setup, up the line pressure, aftermarket trans cooler, performance 2800rpm stall convertor, and you have something that will come off the line like a screaming banshee, shift positively, and take the Lion's share of 1000hp.
Most cars up to Super Stock use autos, go above that and you're likely to see Lencos (which bare little relation to a regular manual trans - they have a transbrake and everything). A Super Stock car needs to come off the line reliably to hit the bracket ET right - doing that with a regular manual trans is very difficult, especially when you need a Swartznegger sized leg to control a clutch that can take the power they're putting out.