I'm wanting to use the optional Armor as Damage Reduction rules, but there is nothing listed as how it interacts with rules based on AC such as touch attacks and the like. I know that touch attacks still go against touch AC but does this change "nerf" the characters that use touch attacks as a perk?
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Touch attacks are generally used by spells and the such as they would bypass the armour, affecting the person whether they have hit their armour or flesh. For anything else I think it would depend on the situation and you would need to look at the specific intent behind the perk and try apply that in a real world situation. That should help figure out how to handle it with these rules.
I can't think of any specific feats that would be affected off the top of my head (if you could provide a link to the specific perk that prompted this question that would be great) but as an example if a feat allowed someone to hit touch ac rather than normal ac, you could interprete that as someone being skilled enough to find the chinks in their opponents armour. You could translate that into the Damage Reduction rules as making their attacks bypass the DR from the armour as they find their way past it.
As you can see they don't have to be nerfed, but without specific examples of rules you are concerned with it's hard to say and you'd probably need to make a case by case judgement as DM.
Edit to deal with specific instance
The OP has given the Magus ability, Arcane Strike (Ex) as an example of how would it fit in these rules. If I look at how it would work in the original world, turning a normal attack into a touch attack is bypassing the AC. This can be thought of as making an attack magical, in that even if it touches the armour it will still do damage as if it had bypassed the armour, the magic coursing through the armour and into the enemies body.
Take that through to the Damage Reduction rules and you can apply it the same way by making the weapon one stage better at beating DR. So a non-magical weapon becomes magical for overcoming DR, and a magical weapon becomes adamantine, etc. At higher levels you could even make the weapon bypass all DR except epic DR.
Touch attacks are usually energy attacks, which are not affected by DR (rather, they’re affected by Resistance). As such, there’s not much interaction to speak of: touch attacks still roll against touch AC (which is still a thing even under armor-as-DR rules), and then apply their effect on the target on a hit. The effect usually ignores DR.
If you found a touch attack that deals physical damage (something that allows weapon attacks to operate as Touch, a strange spell, whatever), then that would be reduced by DR. It would probably bypass Resistance, though.