[Edi]

Yes. You're confusing weapon inherent penalties with ambidexterity penalties.

Ambidex bonus affects penalty due to weapon length, meaning adex 2 would negate the weapon length penalty for axes (length 1), so the double axe warrior would have only -1 penalty to attack courtesy of the inherent penalty of the axe. If they used double maces, there would be no penalty at all. The sword/axe warrior would have a length penalty of 3-2=1 and would get another 1 poinyt penalty for the axe, so his attack with axe would be at -2 to basic attack and the word attack with -1 to basic attack (with the second attack being effectively 2 points higher due to the def penalty for the first one).

Increasing ambidex bonus is more effective if the weapons being used are long and if there are no inherent attack penalties for the weapon. I'd actually prefer a +2/+1 att/adex bonus, that would have an impact that still would not be too overpowering.