Ok, putting my mechanical engineering hat on:
When trying to match a body and neck, if both pieces have a similar resonant frequency, then that would enhance the amount of vibration you feel through the guitar, making it 'sing' more, but perhaps it might also make deadspots more common, since the body and neck transfer energy away from the strings at this resonant frequency.
So you might have two design aims in mind: choose two pieces that are as close as possible in resonant frequency; or the opposite, choose two pieces that are as far apart as possible.
His method however does not fit with either of these two aims. Matching the highest pitch neck with the lowest pitch body, and the lowest pitch neck with the highest pitch body, would end up with a wide range of results, with some pairings resonating together and some not.
I'd be less inclined to say it's bollocks if he actually explained things properly, but he doesn't appear to understand what's going on well enough to do this.