Actually, in your original post, you were knocking the 1/4 mile elapsed time and said nothing about the speed. Not that this changes anything.
You're not getting it- the reaction time has nothing to do the elapsed time. Think about it this way: You and a friend have identical cars- weight, power, etc. is all perfectly identical. You both are going to drive your respective vehicles to a neighbor's mailbox that is precisely one quarter of a mile away from your mailbox and you want to time how long it takes to get there. The clock starts as soon as you pass your mailbox and you are both parked in the street, side-by-side, just before the mailbox. Your friend floors the pedal in his car and his stopwatch begins ticking as soon as he passes your mailbox. He gets to the neighbor's mailbox and his stopwatch shows that it took exactly 20 seconds to get there. Now, you take 2 minutes to finish your drink, then you floor the pedal in your car. You reach your buddy at the neighbor's mailbox and your stopwatch shows exactly 20 seconds, yet, you are 2 minutes behind him. Does this mean your car is slower because you got there 2 minutes and 20 seconds behind him? No. You just had a 2-minute slower reaction time. But the time that you were actually racing from your mailbox to the neighbor's was 20 seconds- exactly the same as his.
Now, picture the same scenario, only your car now has a supercharger. Your friend's car is still as it was. He gets to the mailbox in 20 seconds again. You take 2 minutes again, take off, and get there in 15 seconds this time. Does this mean you are still slower because you arrived 2 minutes and 15 seconds behind him? No. Your reaction time was still 2 minutes. But the time that you were actually racing from your mailbox to the neighbor's was 15 seconds- 5 seconds faster than your friend's car. Your car is 5 seconds faster over a quarter mile distance than your friend's car. When you started your race versus when your friend started his makes no difference.
Look at it as there being two timers in a race. The light goes green and a timer starts from then until the car trips the beam at the start. This calculates the RT. There's a second timer that starts simultaneously when that first timer ends and it is stopped when the car trips the beam at the 1/4 mile mark, giving the 1/4 mile ET. The timer that tells how fast the car is is the ET timer. The RT timer just shows how long it took for the driver to respond to the light turning green.
No, numbers don't lie. But your misunderstanding of them doesn't tell you truth, either. The video really means nothing in this comparison unless it captures all that happened in both runs- if the driver was at WOT when the truck tripped the beams, if the tires didn't grip as well on one run versus the other, if the wind changed directions from one run versus the other, etc.
In reference to that video, if that guy stomped the pedal to WOT during both races (regardless if he stomped it immediately after the green light or waited 2 minutes then stomping it), then the results are valid. If the light went green and he gently rolled onto the throttle the first 10 feet or so of the untuned race, then this would skew and invalidate the results. There are always small variables (a head- or tailwind in one race but not the other, a warmer engine having it's timing retarded,etc.) that will happen. This is why it's necessary to make a few runs pre-mod and a few runs post-mod to get an average. The more consistent the vehicle and driver are, the more accurate the before and after comparison results will be.
NOW, to be technically accurate, a tune can alter the RT: Say this driver can stomp the pedal precisely on the millisecond that the light goes green every time without fail. The truck, untuned, may not respond as quickly due to the throttle being opened more slowly because it has an electronic, computer-controlled throttle. The throttle response tables can be tuned to open the throttle more and/or more quickly when it receives a signal from the pedal that it has been floored and commanding 100% throttle. Yes, there are many other things that can be tuned to reduce the response time, such as the injector and ignition timings, but let's keep it simple here. This would make the truck jump milliseconds sooner when the pedal is stomped, resulting in the start beam being tripped sooner.