i actually like automatics much better than manuals ( just my opinion) as far as an automatic turbo... just look at mr. Tigers car you can turbo an automatic but if you plan on running a lot of power through the engine then you will probably run into some trouble, if you are going to turbo an autimatic you can save your tranny a lot of wear by improving the transmission fluid cooler, there are aftermarket coolers available, you coulc also look into a better tourque converter, www.importperformancetrans.com has transmission build kits available for the 1mz-fe as well as cooling kits and tourque converters
edit: oh and as far as power there will be a difference in gear ratios of course
With a torque converter setup up to your powerband (stall speed and flash speed) along with a higher torque multiplication factor and the tranmission having upgraded clutches and springs to shift faster, and hold more power. A built A/T will beat a manual.
It does not drop boost between shifts because you do not let off the gas, you launch at your powerband AND with less wheel slip. Built A/T's shift faster than people can, and don't miss a shift. Also, keep in mind that any time the torque converter locks up, it's running the same effeciancy as a manual. (WOT through the top of gears) You also have a much higher torque multiplication factor anytime that you need it. (Such as right after the quick shift now that the engine has freewheeled ahead of the convertor, the convertor will now catch back up to the engine. So you get a fraction of that power back during the shift)
Now what advantage does a manual have in a straight line vs a properly built up A/T? I don't know.