I know that all worn armor counts when calculating encumberance. Some pieces of armor have special rules, like FFBA or Mil-spec armor, and the optional rule for custom tailored armor as well. What about armor thats physically part of the character? Orthoskin and Dermal Plating? Cyberlimb armor? Bone Lacing? A Troll's natural armor? I can't find anything that says they don't count so by default they do, but it feels wrong somehow and I can't help feeling that I'm missing something.

The encumbrance rules specifically talk about armor that the character is wearing. Armor that is part of the character is not worn, so it doesn't fall under the encumbrance rules.

It would be hard to be encumbered by one's own skin. If it's something like plating, I think the assumption is that you get used to it while you heal from surgery