You do make a point, however don't forget that the NSX Type S's last production was in 2005 and the S2000 is still being produced as we speak. There is no doubt that the CTR is fast but to outperform other cars that have better power to weight ratio as well as better weight distribution is a bit suspicious. In terms of marketing, Honda wouldn't make a cheaper car faster then its higher performance as well as higher priced cars because its simply not smart in terms of marketing a product. If you watch the lap time on that video you can see the fastest lap time made by those cars and it still seems that some drivers were "sandbagging" their cars.
You're right, looking at an older episode, I see that the NSX Type S has done 1:05.83 in the past where it is doing about 1:07.66 in the newer episode. Given the difference that weather makes (say about 1+ seconds between a cold and warm day), it seems like the difference is slightly larger than you would expect. The drivers are different as well (Tsuchiya for the older one, Iida for the newer one), although I think almost all the drivers are pretty competent, considering they are paid professionals. We must also consider that the primary mission of the races is to illustrate the differences between the cars and to show the viewers how they compare, although the time attack laps are supposed to provide the timed benchmark for lap times.
On outperforming cars with a better power to weight ratio and better weight distribution--of course you can achieve that! It's all about how you set up the suspension, select tires, and lighten the car--it's all about cornering speed. That counts for quite a lot and easily makes up for any deficiency in straightline speed. And as we saw on the back straight, the Civic was no slouch there either. If Honda did make the Civic faster than the S2000, then it's something to be praised. Maybe that's why the S2000 CR is coming, with beefy suspension and the same sticky tires as the CTR has.
An interesting comment after the race is that the S2000 and the rear drive cars were fun to drive, while the Civic was not as fun. Their conclusion was that with the new CTR, Honda gave them the impression that it was all about speed and to never mind about having fun. The S2000 driver was also being ribbed about how he kept missing shifts.
Despite the lap time discrepancies (and only with the NSX), I think it's really, really hard to believe that somehow the drivers are coordinating and conspiring to make only Hondas look good. There are too many other episodes where other cars look good. i.e. see the introduction of the RX-8, 350Z, Skyline R34 GT-R. There have been episodes where they really criticized a car, like the MG-F. The drivers are also different from episode to episode, like Yuji Ide in this CTR episode.
Okay, I just looked at another episode (review of the Cayman), and the NSX Type S does 1:06.0, the S2000 does 1:08.93. The 350Z is 1:08.71. These times are pretty consistent with the older episode I checked above.
Here are the Tsukuba lap times across three BM episodes. Only the NSX was in all three.
NSX Type S: 1:05.83, 1:06.0, 1:07.66<-CTR intro episode
S2000: 1:08.78, 1:08.93
350Z: 1:08.71<-older model, 1:07.87<-2007 model with VQ35HR engine
