It probably is a reflection of the _cabin_ flown in - rather than the fare paid. I noticed it on my AF boarding passes last week as well - so it may be an element of the alignment (i.e. any Y-type fare on the JV partners shows printed as Y), etc...

And, it makes sense why it would print the highest of the fares - as they are pretty harmonized across the JV (Y for coach, J for biz, F for first)... No CoS bonuses though :-/