Interesting thread that seems to be dealing with an argument involving theory v.s. application.
In terms of pure theory, I would agree with the physics junkies. However it is possible that given the average riders skill set, gearing changes such as the one CIP has made could provide for an easier application of torque/power in tests such as this. It is certainly conceivable that the lower stock gearing makes it harder to get a good launch — ironically, due partially to the faster acceleration. You also have to be prepared to make that first shift much sooner and if you make a less than perfect shift you'll cost yourself a measurable amount of time. Such variables have quite an impact on short runs like those that CIP is making in the videos.
In a perfect world, a lower geared bike is going to outperform the higher geared bike in terms of pure acceleration. But insert less-than-perfect humans, road-surfaces, etc. into the mix and you begin to throw things off balance. A professional racer that can achieve a perfect launch and make lightning-quick shifts is going to have different results than the average guy trying to mimic the more skilled rider. Three different riders might well prefer three different gearing setups to achieve their best times from 0-60mph, 0-100mph, etc..
Another way to look at it: If the CB1100 came with an eight speed transmission and lower gearing, in theory you would have the potential for impressive acceleration. In reality the difficulty of launching and the inefficiency of shifting would overcome the gains provided by the low gearing in a test of 0-60 times for example. In terms of real-world applications, I'm guessing the average rider is much more concerned about roll-on acceleration at varying speeds than 0-[insert speed here] times. But tests such as those CIP is running makes for an interesting conversation.
Bottom line: Others might experience different results, but this gearing change works out better for CIP57 and makes his CB1100 experience even more enjoyable. That's good in my book.
All of the above is simply my own opinion of course and it's worth the same $.02 as anyone else's.

I just realized that I somehow missed AzBob's post (#23) which makes much of mine appear rather redundant and much less eloquent. I'll just scramble back into my cave now.