In the handbook they also point out "these are affiliates are not spam" - and they give a few urls of the large shopping mall type sites - like shopping.com . So they don't say that all affiliates are bad, just the thin ones.
I am surprised to see that they actually use humans to rate sites. I have heard it before but never believed it since it seems so labor intensive. This doc sure goes into detail what to look for. But basically you have to think users first and monetizing later. You especially come under scrutiny when you are sitting on page 1 of the SERPs. Better have the ship in order to stay there.