Checked the book about the rating system.
It says it rates only complete sets, with box. Doesn't say wether the box is opened or not.
About the ratings: it is only about rarity and explicitly not about collectors value or how much a set is wanted by the buyers or collectors.
How the rating is actually done is not explained. It is indeed rather vague. The specials for instance: specials from the same series, produced during the same year, sometimes have different ratings. Were the not produced in equal numbers? See for instance the first series with perfor-box. The vulture with bones, third in the series, is more rare than the others. Was it produced in lesser numbers?
Riddles riddles. Why don't we ask the writers?