I'm starting a Pathfinder Campaign with the alternate rule for armor as damage reduction. I'm just wondering what gets changed to damage reduction and what stays defense. For example, a shield's AC goes into defense, but armor's AC goes into damage reduction, as does natural armor, and can be bypassed by magic. What about things that don't list a specific type of AC bonus, like mage armor? It gives you +4 bonus to armor class; does that go to defense or damage reduction?
The spell Mage Armor does specify the type of AC bonus:
Therefore, Mage Armor adds to armor DR.
Almost everything should clearly indicate what kind of bonus it grants, which will make it clear whether it applies to Defense or to armor DR. Pathfinder aimed to fix a lot of the deficiencies that d20 had accumulated, and diligently typing every bonus that needs typing is one of the things that Pathfinder is pretty good at.
The rare exceptions of ambiguous untyped bonuses (such as when using some of the lower-quality 3rd-party d20 material in PF) can be sorted out by common sense or simply your preference. For common sense sorting: anything that absorbs the damage from a blow that has already hit you goes to armor DR; anything that prevents the blow from connecting with its target in the first place (shields being in this category) goes to Defense. If you're lucky, something that adds an ambiguous untyped bonus to AC will say whether it adds to only Touch AC or never to Touch AC, and then it clearly applies to Defense in the first case and DR in the second. Such ambiguous untyped bonuses will be the exception though – as a general rule of thumb, unless it's an armor bonus, it falls under "other modifiers" in the Defense equation.
Mage Armor Goes to DR
Mage armor provides an Armor bonus to AC, and therefore goes to DR, not Defense. The rule states that
Thus all Armor bonuses go to DR.
Meanwhile, Defense is defined as:
Mage armor does not actually have any Enhancement bonus to its Armor bonus to AC; it just provides a flat Armor bonus to AC. Thus no part of the bonus goes to Defense.
Adjudicating any bonus from any source
Since there has been some confusion on this point, I want to clarify. There are two separate rules here, one that covers Defense and one that covers DR. They each provide coverage of any possible AC bonus and eliminate even the possibility of ambiguity.
Is the bonus to AC an Armor or Natural Armor bonus? If not, it is added to Defense.
If yes, the next question is: does that Armor or Natural Armor bonus have an Enhancement bonus to its own bonus? This happens when you have magic armor, or the barkskin spell, or whatever. If the Armor or Natural Armor bonus has an Enhancement bonus, that applies to Defense. Any portion of an Armor or Natural Armor bonus that is not derived from an Enhancement bonus does not apply.
Note that this has nothing to do with straight Enhancement bonuses to AC. Those go to Defense because they are not Armor or Natural Armor bonuses, but they are not the same as Enhancement bonuses to another bonus, namely the Armor or Natural Armor bonus to AC, as discussed in the previous paragraph.
So we have a little flow-chart:
This covers all possibilities: a bonus is either (Armor or Natural Armor) or it is not. Ambiguity is logically impossible here.
This one’s even simpler:
Once again, a bonus to AC either is (Armor or Natural Armor) or it is not.
Note that since an Armor or Natural Armor bonus to AC can include an Enhancement bonus to that bonus, and such Enhancement bonuses to Armor and Natural Armor count towards Defense, such Enhancement bonuses have the unique property of “double-dipping” – they count both for Defense and DR. Again note that this is Enhancement bonuses to Armor or Natural Armor bonuses. An effect that directly applied an Enhancement bonus to AC would go to Defense and not to DR.
Untyped bonuses are not a mistake or problem in a d20 system. Since they tend to stack with one another (unless they come from the same source), they can be a balance issue, but the lack of type does not mean that they are somehow ambiguous or undefined: untyped bonuses are a normal and expected part of the system. In this case, being untyped, they are neither Armor nor Natural Armor bonuses. As such, they apply to Defense and not to DR.