The lesson is saying that with と both sides of the comparison have equal weight. There is no standard that the other is referenced against. They both share the same characteristics.
With に the lesson says that this is marking the standard of comparison. It is the thing that something else is compared to. In this case the father should be the standard of comparison and be marked with に. It makes sense to say that the son resembles the father, but it's a bit weird to say that the father resembles the son.
I guess in English you could translate その父は息子と似てる as "the the father and son look alike", whereas その父は息子に似てる would be "the father resembles the son".
In summary, 31d is fine because no standard of comparison is being made.
Actually, I see what you mean now. The part that says "they both make the second person the basis of comparison when ...". That's confusing.
I think 31d is fine, but better wait for someone more knowledgeable to give a definitive answer.