I found this good explanation, on another site, why auto-equipped Challengers are faster than manuals when drag racing. What is perhaps different from the manual, is that the timing does recover more reliably on the auto, as soon as engine load resumes for the next gear. That is where some manual owners have encountered "trouble" as far as optimal performance. One theory in circulation on this matter is that the knock sensor happens to pick up noise from somewhere in the drivetrain or clutch mechanism during a violent shift event that is detected as knock. So the computer will naturally dial back momentarily as a precaution. Timing doesn't come back as quickly as desired, and that manifests as lost performance over the course of the run. The manual drivers not only get hit with the inevitable shift event, but sometimes also the aftermath of a shift event which the engine unfortunately interprets as knock. I don't know if it has ever been tested in such a way, but it seems like this sort of behavior would encourage manual drivers to shift smooth, if they are going to shift fast. If you just crowbar the stick into place and whip the clutch with little finesse, you won't be rewarded for it. The part where autos get a distinct leg up on track times is that the shifts are interleaved (much like the latest DCT style "automated manual" gearboxes). Mechanically, it is like a 0 msec shift event, whereas on the manual, a good typical shift event may take upwards of 300 msec each time. When manual drivers have to do it 3x over the span of 1/4 mi, it's enough to add up. That's 900 msec in the race where the driver is literally just coasting the car (off-throttle).
There is a "timing event" that happens with the manual shifting in the Challenger. It is programmed to retard timing briefly when shifting. I do not think the autos have this. Plus the autos do shift more quickly. Still would rather have a manual.
I have a question, is there custom tuning capabilities available from say HPTuners that would allow someone to adjust the timing event in the manuals to help to improve this?