On the face of it, it is rather odd that currently someone may be extradited from HK (a territory of the PR China) to, say the US, but not to mainland China.

That's why it's a question of integration. If HK were fully integrated with the PRC, requiring an extradition treaty at all would be strange. But it isn't integrated and the protesters evidently want to keep it that way.

I don't know how many Puerto Rican separatists there are, but they would probably oppose extradition to the United States.