Nowhere in DMG2 (which is the only rules reference that mentions it) are the inherent bonuses classified as enhancement bonuses. In fact, nowhere in DMG2 are they even called "inherent bonuses." The only place you can find "inherent bonuses" by name is the CB, and the CB implements them as enhancement bonuses.
Keeping that in mind, what's actually being argued about is a roughly outlined house rule in DMG2 that was implemented differently in the CB--which, as we know, isn't a rules reference.
So you'll have to forgive me if I think this debate is a little misguided.
So for what...the 4th time in this thread (starting in post 3 or 4)? I don't own a copy of DMG2 so maybe if someone who does would post the rules blurb on it. Inherent aside, the other debates have been interesting.