Wow, this was going well for a while, but it sure blew up today.
My view on the "fairness" of the comparison is that they compared the highest-performance version of the ND to the highest-performance version of the BRZ. The fact that, for the BRZ, the top trim doesn't gain any performance over the base model, is not Mazda's fault. As others have said, the price was clearly stated, so I don't have a problem with MT's presentation.
I also don't think the BBSs and Brembos added a ton of performance. Nor do I think they're likely worth the $3400 -- I agree with MT on that point. As I said in the thread opener, I think tires played the biggest role (certainly more than the ND's trim level), and the Primacy HPs aren't Mazda's fault, either.
Really, at the end of the day, the lap times are in the same ballpark, and I don't think it matters which one is faster. When I'm driving my NB at Summit Point, I'm not even timing my laps, just bombing around enjoying the chassis.