[RPG] How does the Multi-Weapon Fighting feat ‘replace’ the Two-Weapon Fighting feat

In short, you are right and misinformed. The general rule is, when the situation fits the rule, and there is nothing in another rule to counter that, then you interpret the situation as in that rule.

In your case, when your off-hand weapon is light, -2/-2 is applied with TWF, and -4/-8 without it. Nowhere in the rule calls for the kind of weapon in the main hand, so you apply -2/-2 or -4/-8 (without the feat) no matter you are wielding a short sword or a longsword in the main hand.

There are no rules regarding over-sized weapons and using more than two arms. Normal over-sized weapon penalties apply.

Inappropriately Sized Weapons: A creature can't make optimum use of a weapon that isn't properly sized for it. A cumulative –2 penalty applies on attack rolls for each size category of difference between the size of its intended wielder and the size of its actual wielder. If the creature isn't proficient with the weapon, a –4 nonproficiency penalty also applies.

The measure of how much effort it takes to use a weapon (whether the weapon is designated as a light, one-handed, or two-handed weapon for a particular wielder) is altered by one step for each size category of difference between the wielder's size and the size of the creature for which the weapon was designed. For example, a Small creature would wield a Medium one-handed weapon as a two-handed weapon. If a weapon's designation would be changed to something other than light, one-handed, or two-handed by this alteration, the creature can't wield the weapon at all.

The rest of this answer assumed multiple greatsword (or other two handed weapons).
You cannot use the Two-Weapon fighting feats if you are using more than two arms. You need to use the Multi-weapon fighting feats. If you were fighting with two greatswords, one of them with be primary, the other offhand. Likewise, if you had sixarms, two for the weapons would be offhand, and so on. You will always have one primary weapon.

Multiweapon Fighting (Combat)
Prerequisites: Dex 13, three or more hands.
Benefit: Penalties for fighting with multiple weapons are reduced by –2 with the primary hand and by –6 with off hands.

Stealing the table from this answer you would make your all your attacks at -4 regardless of if they were off-hand or primary: Table: Multi-Weapon Fighting Penalties

Circumstances             Primary Hand  Off Hand
Normal penalties               –6            –10
Off-hand weapon is light       –4            –8
Multi-Weapon Fighting feat     –4            –4
Off-hand weapon is light and
Multi-Weapon Fighting feat     -2            –2

I have found no rule which changes the damage modifier (*1.5) from high strength.

Likewise, power attack applies to all attacks as described, there are no special rules for using more than one two handed weapon. The primary great sword would get +3 per -1 penalty. The off hand greatsword would get +1.5 per -1 (rounded down, so +1, +3, +4, +6, etc. ) Emphasis all mine.

BONUS HOUSERULE: I would not allow a creature to use a weapon who's category was more than two handed, as per the normal rules. However there are items in 3.5 that required more than two hands to use ( I think it was the scissor sword ) and had better stats. I would also allow a creature with more than two hands to substitue the Multi-WF feat in place of the T-WF for classes with bonus feats, such as ranger.

Have a look at the Gythka and Scissors Sword, which are four handed and six-handed weapons from Savage Species (I know, not pathfinder) on page 45.