10K resistors avoids additional current consumption, if the input OCT is activated. It's also said, that the 10K resistors should be placed near to the inputs. How many resistors are used is a matter of most convenient routing, I think.
An interesting point with the transceiver and reference clock input termination suggestions is that they give up the idea of a differential DC bias for unused receivers, that has been e.g. recommended for Arria in datasheet updates. I hope, that Altera engineers don't reveal belatedly an excessive current consumption as they did in the previous case.