No, it doesn’t. Note, however, that the penalties are different.
In Chapter 8, they are talking about penalties that are applied to every attack in the full-attack where you use the Two-Weapon Fighting combat option. If you have the Two-Weapon Fighting feat and are using a light weapon in the offhand, when you use the Two-Weapon Fighting combat option to get an extra attack with your light weapon, all attacks in that full-attack take a −2 penalty.
For instance, if you had BAB +5, no other bonuses to attack, the Two-Weapon Fighting feat, and you chose to use the Two-Weapon Fighting combat option with a light weapon in the offhand, you would make two attacks, the first an attack with the main hand weapon at +3, and then a second attack with the offhand weapon, also at +3.
The penalties described in the Improved and Greater Two-Weapon Fighting feats apply only to the new attack those feats grant.
So if when the above character got BAB +6/+1 and took Improved Two-Weapon Fighting, the −2 penalty from using Two-Weapon Fighting at all remains. The same main hand attack, at +4 now, and offhand attack, also at +4, remain. There is also an iterative attack from high BAB, at −1, and then Improved Two-Weapon Fighting effectively gives an “iterative” to the offhand attack, so you get another attack at −1. So in total, +4, +4, −1, −1.
At BAB +11/+6/+1, with Greater Two-Weapon Fighting, the same kind of thing happens: you take a −2 penalty across the board, and Improved and Greater Two-Weapon Fighting each give a bonus attack that mirrors the +6 and +1 iteratives, respectively, so you get two attacks at +9, two at +4, and two at −1.