I had the same feeling after reading this "For flights marketed and operated by a partner (partner two letter code precedes the flight number), and booked on alaskaair.com, see chart below in Earning on Partner Flights booked via Partner Sites for mapping of fare class to cabin by partner.".

However, this states nothing about the actual earning. It just points to the mapping of partner fare class to fare type for earning (i.e. International Business, First, Economy, Discount Economy, etc). So if you have a partner coded and marketed flight, bought on the AS website. the partner fare code table tells you how it will earn according to the 'bought on AS website' rule.

So IMHO there is no contradiction at all. Agreed they could have worded this a lot better...