some manuals transmissions are better geared than the equivalent auto/pdk for performance. some aren't. F80 for instance has good ratios for the manual... the ratios for the dct will leave you scratching your head as they don't make much sense. the last thing the car needs is a shorter 1st gear ratio.
turbo auto/dct cars have a big advantage as they don't lose boost between shifts.
manual NA cars, like the GT3, don't have a huge advantage with a pdk aside from 0-60 and consistency around the track. The manual has a no-lift-shift mechanism that lets you shift with the throttle pinned. how quick it goes just depends on how quick you can kick a clutch.
** aero is probably playing a slight role here. but youre not seeing the pdk RS leap forward a ton (maybe foot) every time the manual gt3 shifts.