Empty Hand Mastery
For those unaware, in the campaign Oriental Adventures, there are other "unarmed" feats that you can take (many of which are extremely interesting and fun for monks, like Defensive Throw).
In addition, they have "School Masteries" that you can earn by following certain feat progressions. For Empty Hand mastery, a monk has to take a bunch of feats that normally would have no real benefit to the class when in combination, but the overall effect is that you increase your damage-dice one level, just like Improved Natural Attack... only much more costly.
Knowing this information, I'd say that it makes a pretty good argument that since 3.0... unarmed strikes very well probably weren't considered natural weapons. Or... if that's not true... well I don't think PC's are 'supposed' to take feats from the Monster Manuals, etc., anyway (do you allow your PC's to also take Ability Focus for the Stunning Fist abilities).
In terms of the hit dice being two high or unbalanced... I couldn't disagree more.
You presented averages for damage, which is cool and informative. But you also completely left out the part about a Fighter's generally superior AC and AB. Monks, even just using core, standard rules, have always had higher damage averages than fighters to a degree, and they've also always hit far less often, and get hit more often.
This isn't to say that monks are poor at higher levels. While I would agree that Improved Natural Attack is a bit of a gimme feat for monks, we could also go through the many books with feats and come up with interesting fighter damaging combinations as well. So I still don't believe a monk getting more damage progression is that out of whack. They've always relied on getting multiple attacks and, when actually hitting, creating devestating effects like stunning, or doing lots of damage.
At the end of the day, a monk only has a Rogue BAB progression with extra stacking attacks when using Flurry of Blows (which clearly gets helped out by a Monk's Belt if you just allow monks to pick up whatever magical equipment they want in your campaign).