Trying to put some flares in the road, just had a friend and I hit this particular pothole, so filling it in a bit and laying flares...
That's the signpost up ahead, you've just passed into...
The Natural Weapons Zone.
Apparently the Natural Weapons issue is still too hard to find answers to. When (as just happened) two smart guys read the same thread, with the same posts by the same dev, and come away with different answers... then the answers are still hard to find.
Maybe that's because nobody (well ok, the devs) is ever thinking of the system as a whole, because we've all got our own interests whenever the issues come up. So we're all automatically looking to confirm or deny something we want or don't want. So well-intentioned guidelines become tripwires.
So I'm setting a goal of covering some of the possibilities for Natural Weapons, in the hope that I can get a dev to confirm the compiled clarification.
So what follows is my understanding. Please correct me, or confirm.
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The source of your natural weapon will tell you the damage, the damage type(pierce/slash/bludgeon), and the primary or secondary status of the natural attack.
And that's where begins the confusion that brought me here. The damage stays the same, or anything changing the damage declares itself clearly. The damage type stays the same. But the Primary/Secondary thing? It's changeable. And the changes aren't marked well.
Not changeable by a feat, or a class feature, or anything you really control. The change is based on the number of Natural Weapons you have, and whether you're using them with other (manufactured) weapons.
If you only have one NW, and use it alone, it will always be at full BAB, and 1.5*STR to damage. I would guess the devs are thinking a parallel to a two-handed weapon, here. It doesn't matter whether the one NW is 'Primary' or 'Secondary', because it's _only_, so it's treated superiorly, even better than Primary. This changes if you use the NW with other manufactured weapons. In this case, too, it doesn't matter whether the NW is Primary or Secondary, because using the manufactured weapon makes it Secondary.
A couple of examples are in order:
Slappy the Alchemist-Clown has a tentacle (defined as secondary, but it is his only NW) attack, and a poisoned dagger, readied in one of his hands, but held behind his back, hidden in a bouquet of flowers. (That wacky Slappy...) If Slappy attacks with only the tentacle, he uses his full BAB and gets 1.5*STR added to damage. Or if Slappy instead attacks with the dagger, the dagger uses his full BAB, 1*STR added to damage. On the turn he attacks with the dagger, he can also attack with the tentacle at -5 to BAB, .5*STR to damage.
Poochy is Slappy's partner. Same tentacle, same dagger. (They were on sale) But Poochy has a magical set of vampire fangs that give him a bite (primary) attack. Poochy can attack with the bite alone, and he'd use full BAB and get 1*STR to damage. He can also attack with bite and tentacle, the bite at full BAB, 1*STR, and the tentacle at -5 to hit, .5*STR to damage. But being very fond of his poisoned dagger, Poochy prefers to attack with it, and bite, and slap with his tentacle. The dagger is full BAB, 1*STR for damage, the bite at -5 to hit, .5*STR for damage, and the tentacle at -5, .5*STR for damage.
If you have multiple NW, all the 'Primary' NW will all be at full BAB, and 1.0*STR to damage. All the 'Secondary' NW will all be at -5 to hit and .5*STR to damage. And if you pick up and use a manufactured weapon, all your NW, whether Primary or Secondary, are at -5, and .5*STR to damage. You can hold and not use a manufactured weapon while attacking with your NW attacks, but you cannot use a NW based on the same limb used to hold or wield something.
To sum up: There are really three kinds of Natural Weapons; Primary, Secondary, and 'Only have one'. Primary is full BAB, 1*STR bonus to damage. Secondary is -5 to hit, .5*STR bonus to damage. And 'Only have one' is full BAB, 1.5*STR bonus to damage. And using a manufactured weapon makes ALL Natural Weapons into Secondaries.
I think. :)