A short sword is a light weapon. The Rogue can PA with it if he likes, but he won't get any extra damage so its not his best move.
You're arguing semantics and ignoring the point I was making. Forgive me for having only my PHB 3.0 handy when I made that analogy and believing that people would have enough insight to understand the point I was attempting to get across.
Where are you getting this from?
Grammar, sentence structure, logic, reasoning, extrapolation. Take your pick.
But a snake's poison is a 'special effect', and as such is negated if you don't get through the DR.
True. And because the reasoning behind SA bonus damage is damaging a vital organ, body part, etc., if that organ is not damaged by the initial attack, no SA bonus damage. It's no different than if the creature had no vital organ.
See if you can follow this, glass:
A) SA damage is bonus damage inflicted on an enemy as a result of a precise strike by the rogue targeting and damaging a vital organ.
B) If the vital organ is not damaged by his precise strike, then the rogue inflicts no SA bonus damage
C) If a vital organ is damaged by his precise strike, then the rogue inflicts SA bonus damage.
D) DR protects all parts of the body equally, including vital organs.
E) If the damage of an attack does not exceed (inflict more damage than the DR protects) or bypass (by using silver, magic, holy, etc qualities) the DR, then the attack inflicts no damage to the body (including vital organs) of the creature with DR.
F) If the damage of an attack exceeds or bypasses the DR, then the attack inflicts damage on the body (including vital organs) of the creature with DR.
Both statements A and D are true. B and C can be logically reasoned from A, the same with E and F from D. So, if E, then B and if F, then C.
To not allow the SA damage is basically saying that you wouldn't allow a Critical Hit, because a critical hit is "bonus damage".
No true at all. They are very similar but still different things. A critical hit is basically the weapon doing more than its normal listed damage but it is still the damage from the weapon, not from the location of its point of impact. While SA is damage specifically due to striking a vital organ (or some other specific location; vein, artery, joint, etc).
If you need an analogy to visualize this difference, here goes:
The rogue (str 12, using normal longsword, SA +2d6) attacks a werewolf (DR 10/silver). The rogue scores a normal hit. He rolls 4hp damage for the sword, +1hp damage for his strength, doing 5hp damage. This is less than the DR, so no damage is inflicted.
The next round, the rogue threatens a critical hit. It is confirmed. The rogue rolls 7hp for the sword, +1 for his strength, and then X2 for the critical hit, for a total of 16hp damage (7+1=8, 8X2=16). The damage from the rogue's sword beats the DR by 6, so the werewolf takes 6hp from the critical hit.
The next round, the rogue is able to SA and hits. He rolls 2hp damage for the sword, +1hp for his strength, for a total of 3hp damage. Again, this is not enough to beat the werewolf's DR, so the werewolf is not injured by the attack and because it took no damage (no damage to vital organs or any other body parts), the SA bonus damage is not included.
In the following round, the rogue uses Power Attack for -2 to attack, +2 damage, is able to SA again, but also confirms a critical hit. The rogue rolls 6hp damage from the sword, +2 for PA, +1 for strength, for a subtotal of 9hp which is X2 for the critical hit. His attack with his sword inflicts 18hp damage (6+2+1=9, 9X2=18). This beats the DR by 8 inflicting 8hp damage on the werewolf from the swordd and because it was a SA, which damaged the werewolf (in a vital organ), the rogue adds +12hp of SA bonus damage, for a total of 20hp damage to the werewolf.