I'm no engine builder/tuner and it's been a while since I visited the mototune website -but when I did read it it seemed that much of what he was providing as evidence to prove his case leaned quite far towards anecdotal rather than empirical.
I'm sure that manufacturer break-in procedures are probably on the conservative side, but I have a strong suspicion that the power a bike ultimately makes has more to do with manufacturing tolerances (things like cam timing variances etc) than with how it was broken in.
For the race engine builder to say that because he breaks in motors in hard they make more power -well it seems to me that given the fact that they've (hopefully) taken the time to dial in the motor it will make more power. The hard break-in is likely a necessity - who has time to break in a race motor over a couple of thousand moderate kilometers after each rebuild?
Comparing wear of parts between 2 bikes seems a bit futile unless said bikes were subject to the same conditions, loads and maintenance (all variables identical except for the variable being tested for) over the duration of the experiment.
I take the middle road (I don't wring the piss out of it from new, but I don't lug it around either) and I haven't had any complaints or issues so far. I believe it's a somewhat logical approach, but at the end of the day it's still just my opinion - and worth exactly what I charge for it
I'm not for a second going to argue that a hard & fast break-in is the wrong approach (I really haven't the expertise to do so) but I will happily argue that anything I've seen to date presented as "evidence" to support it really isn't quality evidence